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发表于 10-18-2021 15:26:38 | 显示全部楼层 |阅读模式
I just added a reply to the previous (dated Oct 14) post titled "massively parallel sequencing (MPS)."

Oct 18.2021

(1) I noticed when preparing the posting above that each clone /cluster in Manteia Predictive Medicine's Pascal Mayer and Laurent Farinelli has two kinds )proportion being 50/50) of single strand, corresponding to the two strands of a double-stranded DNA. During the weekend after publication of the blog, I was haunted by how one strand is removed from the cluster.
(2) Just now, I re-read Figure 2 in
Ballard D et al, Massive Parallel Sequencing in Forensics: Advantages, Issues, Technicalities, and Prospects. International Journal of Legal Medicine, 134: 1291 (2020).
, whose caption simply stated, "Subsequently, the 3′ block and the fluorescent tag on the incorporated nucleotide are removed." But how was "3' block" (or strands) removed (as they were anchored, too)?  ("[T]he fluorescent tag on the incorporated nucleotide" can be removed by somehow cleaving it from the last deoxynucleotide incorporated.) Text in this Webpage did not explain, either.

Removing one strand in a cluster is crucial. Otherwise a cluster  would not be a clone.
(3) Method of Nucleic Acid Amplification. Patent number: 9902951; Date of Patent: Feb 27, 2018' Assignees: Illumina, Inc and Illumina Cambridge Limited (in UK, not Cambridge, Massachusetts); Inventors: Eric H. Kawashima, Laurent Farinelli, Pascal Mayer.
("In another embodiment the colonies can be partially digested with a double-strandspecific [sic: should be 'double-strand specific'] 3' to 5' DNA exonuclease (see section E, FIG. 12C, (f)) which removes one strand of DNA duplexes starting from the 3' end, thus leaving a part of a DNA molecule in single stranded form. Alternatively,DNA in colonies can first be heat denatured and then partially digested with an single-strand specific 3' to 5' DNA exonuclease which digests single stranded DNA starting from the 3' end")

There are two types of enzymes that cut DNA (nucleases), exonuclease and endonuclease.

"Exonucleases digest nucleic acids from the ends. Endonucleases act on regions in the middle of target molecules [double-stranded DNAs]."  en.wikipedia.org for en.wikipedia.

There are many exonucleases that remove or eat away a nucleotide one at a time from the end(s) (5' or 3' or both). Nad There are many others who do the same on RNA.

Sam Sacks, A Shaggy-Dog Story from Old Japan; To devour the opening chapters of this Edo-period swashbuckler is to be present at the birth of serie-driven pop culture. Wall Street Journal, Oct 16, 2021, at page C10.
https://www.wsj.com/articles/fic ... ene-lim-11634306294

(i) This is a book review on two new books:
(A) Glynne Walley, Right Dogs or Hakkenden; Part One -- An ill-considered jest. Cornell University Press, 2021 (translation).
(B) Eugene Lim, Research History. Coffee House Press, 2021.
(ii) I do not read the second half of this review, whose subtitle online, but not in print, says, "A swashbuckling epic from 19th-century Japan and an unsettling story of an AI-dominated tomorrow." This gives you an idea what the second book is about.
(iii) In Taiwan, we heard of . Ignorant of its content, we thought it was history, unaware that it was a fiction.

(b) "Kyokutei Bakin's novel 'Nansō Satomi Hakkenden' * * * Bakin, a member of the declining samurai class, wrote during the tail end of the Tokugawa shogunate"  
(i) Nansō Satomi Hakkenden  南総里見八犬伝
(" The eight Dog Warriors [八犬士 (they are human): 犬塚信乃, 犬川 荘助, 犬山 道節, 犬飼 現八, 犬田 小文吾, 犬江 親兵衛, 犬坂 毛野, 犬村 大角], who commonly have family names including the character for '犬' ([Japanese pronunciation for the kanji:] Inu, dog) * * * Bakin borrowed the idea from the Chinese novel Water Margin [水浒传] which was translated and published in Japan at the beginning of the 18th century, and wrote epic fantasies by referring to the historical stories of the Satomi and Hojo clans")
(A) Nansō 南総 is "上総国の別称," whereas 北総 is "下総国の別称." is "下総国の別称." ja.wikipedia.org for 南総 and 北総 is "下総国の別称," respectively. For their locations in Japan, see Nos 59 to 61 in the top map of 令制国
See also (b)(iii)(B).
(B) Satomi
(may refer to: female given name 里美 or "Satomi clan (里見氏), a Japanese clan originating in the Sengoku period")
(C) The kanji 里 has ri as Chinese pronunciation (a measuring unit) and sato as Japanese pronunciation (meaning: hometown). Yes, different pronunciation meaning different things, in the same kanji.
(D) The kanji 智 has chi as Chinese pronunciation, no Japanese pronunciation, and sato in (place or human) name only. From 智美 is derived 怜美, 聡美, 理美, 叡美, 聖美 -- because in names Japanese can switch kanji anyway they want (not necessarily synonyms).
(E) Satomi clan  里見氏
(of the Sengoku period [戦國時代] (1467–1573 [a daimyō 大名 or fudal lord named 織田 信長 'ODA Nobunaga dissolved the Ashikaga Shogunate [足利幕府 (officially 室町幕府, established by 足利尊氏 at 室町 a neighborhood named after 平安京の室町小路, which is present-day 京都市 室町通] in 1573 and launched a war of * * * unification by force' by obliterating other daimyō [kana used in English does not add s to make it plural] and annexed their territories: en.wikipedia.org]) and early Edo period [江戸時代, coextensive with 徳川幕府 (based in 江戸 (present-day 千葉県] (1603–1868). The clan ruled Awa Province as a Sengoku daimyō and was a major military power in the Kantō region [関東地方] during the wars of the Nanboku-chō period. Although confirmed as daimyō of Tateyama Domain [館山藩, centered on Tateyama Castle 館山城 in what is now the city of Tateyama, Chiba] by the Tokugawa shogunate, the direct bloodline [read: males] of the clan died out in the early Edo period
• "里見氏は贈鎮守府将軍・新田義重の庶長子・新田義俊(里見太郎)を初代とする。里見の名は新田義俊が上野国碓氷郡(八幡荘)里見郷(現在の群馬県高崎市上里見町・中里見町・下里見町)に移り、その地の名を苗字としたことに発する。"  ja.wikipedia.org for 里見氏 (citations omitted).
my rough translation: The surname 里見 started with 新田義俊 (里見太郎), who was the first born out of wedlock [by 妾, which is also kanji] 新田義重 [1125 - 1202]. 新田義俊 [whose years of birth and death I fail to find] adopted the place name 里見 as his name. [in Japanese, 苗字 = 名字, simply because the two terms are pronounced the same in that language.)

Hence 新田義俊 is known as 里見氏開祖 in Japanese.

Jim Breen's online Japanese dictionary defines:
* ka-i-san 開山 【かいさん】 (n,v): "founding a temple (on a hill-top)"
• For Nanboku-chō period 南北朝時代, see
The names 戦國時代 and 南北朝 in Japanese history were copied from Chinese history, for similar situations in Japan.
• Awa Province (Chiba)  安房国
(in the area of modern Chiba Prefecture 千葉県)
• han 藩 system
("Han * * * served as a system of de facto administrative divisions of Japan alongside the de jure provinces [han and province is co-extensive] until they were abolished in the 1870s," having started in 1603)

The Ja.wikipedoia.org says the word and idea of 藩 came from China.
(ii) TAKIZAWA Bakin  曲亭 馬琴
(1767 – 1848 (age 81); "Born as TAKIZAWA Okikuni 滝沢 興邦, he wrote under the pen name Kyokutei Bakin (曲亭 馬琴), which is a pun, as the kanji may also be read as kuruwa de makoto, meaning a man who is truly devoted to the courtesans of the pleasure districts * * * His father, Okiyoshi 興義, was a samurai in the service of one of the Shōgun's retainers, Matsudaira Nobunari [松平 喜徳 (1855 – 1891)]" )
(A) There is something wrong to pair, in the page title, TAKIZAWA Bakin with 曲亭 馬琴, simply because Takizawa is NOT 曲亭. Indeed, ja.wikipedia.org explicitly says 滝沢 馬琴 is incorrect, mixing the birth name with pen name
(B) The kyoku is Chinese pronunciation of kanji 曲.
(C) The kanji 亭 has only Chinese pronunciations tei -- meaning the long vowel of te -- and chin (and no Japanese pronunciation).
(D) Japanese-English dictionary:
kuruwa 廓; 郭 【くるわ】 (n): "(1) district; quarter; (2) enclosure; area enclosed by earthwork; (3) red-light district"
   ^ 郭(くるわ) の意味: "1 城やとりで [fort] の、周囲を土や石などで築き巡らしてある囲い。また、その内側の地域。
      2 《周囲を塀 [wall] や堀で囲ったところから》遊女屋の集まっている地域。遊郭。遊里。"
   goo 辞書, undated
   ^ my rough translation: 郭 is the area surrounding a walled city, usually outside but could be inside. From here, the word was extended to mean 遊郭, where 遊女屋 concentrated because 遊女屋 were located in that area  of th4e city wall.  
* The "de" is the location preparation meaning "at" or "in."
* 誠 (P[rincipal]); 実 【まこと】 (adv): "(arch[aic]; modern use is 'makoto ni 誠に']) that's right [or trully]"

(iii) "Satomi and Hojo clans"

They are rival clans. See Satomi Clan
("In 1516, Odawara-based Hōjō 北条 clan defeated the Miura clan and seized Miura Peninsula, opposite of Uraga Channel [浦賀 水道] from Awa Province. Furthermore, the Hōjō expanded northward along Tokyo Bay, capturing Edo Castle by 1524. This threatened the Satomi clan from west and north")
(A) Odawara  (神奈川県)小田原(市)
(B) list of peninsulas of Japan
(section 2 Honshu: East to west are three peninsulas of interest here: Bōsō Peninsula 房総半島 (bō and sō are both Chinese pronunciations of respective kanji 房 and 総; 房総 is from 安房国, 上総国 and 下総国 on that peninsula), Miura Peninsula 三浦半島 (ja.wikipedia.org: 日本書紀 identified it as 御浦 miura, whose kanji later became 三浦), Izu Peninsula 伊豆半島 (named after 伊豆国 there).

日本書紀  Nihon Shoki
(completed in 720)  
was totally written in Chinese characters.

(c) "Bakin came to his enormous success in this emerging milieu by pioneering the yomihon [読本; from Japanese pronunciation (verb yomu, noun yomi) of kanji 読], which literally means 'reading books' (as opposed to picture books) but really refers to the kind of swashbuckling, multivolume narrative fictions that were already a hit in China. In Western terms, Bakin was a bit like Walter Scott, popularizing the historical romance. But the fantastical elements of 'Hakkenden' give it a kinship to those endlessly unspooling fantasy sagas by Robert Jordan or George RR Martin."
(i) "narrative fictions that were already a hit in China"

"中国の白話小説の影響を受けて": ja.wikipedia.org for 読本. Click "白話小説" in the preceding quotation leads to a new page with examples: "主な白話小説: 三国志演義, 西遊記, 水滸伝, 金瓶梅, 紅楼夢"
(ii) Walter Scott
(1771 – 1832; a Scottish historical novelist)
(iii) Robert Jordan
(pen name of James Oliver Rigney Jr (1948 – 2007; American) )
(iv) George RR Martin
(1948- ; American)

(d) "The bulk of Bakin's epic relates the adventures of eight mystically connected 15th-century [in Muromachi period 室町時代] warriors who join together to restore the rule of the noble Satomi clan. * * * the Satomi patriarch Yoshizane [(里見) 義実] is struggling to wrest back control of regions of the Awa province. While threatened by an especially obdurate nemesis, ANZAI Kagetsura 安西 景連, he makes an offhand joke in the presence of his beloved dog Yatsufusa 八房 [kanji 房 has Chinese pronunciation bō and Japanese pronunciation fusa]: If only the dog could bite his enemy to death, he would give it his daughter's hand in marriage. When Yatsufusa [the dog] shows up the next day, eagerly bearing Kagetsura's severed head in its mouth, honor compels Yoshizane to make good on his promise, however humiliating to his family name and to his daughter, Princess Fuse [伏姫, whose Japanese pronunciation is 'Fuse Hime']."
(i) obdurate (adj; Did You Know?  /etymology): "stubbornly persistent in wrongdoing"
(A) The English noun swashbuckle is back-formation from the noun swashbuckler. Which means the noun swashbuckler came into being first.
(B) English dictionary:
* swashbuclkler (n; "mid 16th century from swash+ buckler"):
* swash (v or n; "mid 16th century (in the sense 'make a noise like swords clashing or beating on shields'): imitative")
*  buckler (n)
   ^ buckler
* boss (n; Middle English from Old French boce, of unknown origin): "a stud on the center of a shield"  (The same Lexico page says the boss that is defined as "a person in charge" has a separate etymology: "early 19th century (originally US): from Dutch [noun masculine] baas master.")
(iv) All in this quotation and next (e) are fictional characters (Japanese: 架空人物), except 滝田城 (滝 is kanji for waterfall) which once existed.  (In Japanese: 架空資産 fictional assets, but 架空鉄道 elevated railway)

(e) "A crucial characteristic of Bakin's yomihon, Mr Walley explains, is their mixture of heroic drama with potted lessons about virtue and righteous behavior. * * * The odd couple retreat to a remote mountain fastness where Fuse strives for Buddhahood by reciting the sutras. Her piety is such that, as a holy man tells her, it inspires a kind of mass virgin conception [virgin conception alludes to Mary's production of Jesus; mass, because Prince Fuse, in a sense, spawned eight men] that brings about the eight dog warriors, each born to different families but spiritually linked to Fuse and Yatsufusa. * * * I like the descriptive orotundity * * * Happily, these effects have been used in the jaunty service of nonstop dramatic action"
(i) Japanese-English dictionary:
* fuseru 伏せる 【ふせる】 : "(1) [vt] to lay face down (2) [vt] to point downwards (eyes, head, etc.); to cast down (eyes); (3) [vi] to lie (one's body) face down"
(ii) English dictionary:
* potted (adj): "3: mainly British (of a literary work or descriptive account) put into a short and easily assimilable form  <a potted history of the band's career>"
   ^ "3: briefly and superficially summarized   <a dull, pedestrian [this adjective, not noun, means 'orfinary'] potted history — The Times Literary Supplement (London)>"
   ^ It seems to me that this definition of an adjective comes from its ordinary definition of the verb pot: to put in a verb.
   ^ potted : "English Etymology[:] Adjective meaning 'prepared in advance' first used in a published work by L Susan Stebbing in her Pelican classic Thinking to some purpose [sic; the title should be all capitalized] (1939), where 'potted thinking' is defined as ;a compressed statement to save us the trouble of thinking."
    IDictio, undated
   ^ Susan Stebbing
   (1885 – 1943; a British philosopher; "Stebbing's most popular work is Thinking to Some Purpose (1939), a book commissioned by [publisher] Pelican Books")
* fastness (n; from "Old English Fæstnes (see fast + -ness) ): "a secure refuge, especially a place well protected by natural features   <a remote Himalayan mountain fastness>"
   ^ fast (adj): "Old English fæst 'firmly fixed, steadfast, constant; secure; enclosed, watertight; strong, fortified' * * * Meaning 'rapid, quick' is from 1550s, from fast (adv) , in which entry the attempt is made to explain how a root meaning 'firm, solid' came variously to yield words for 'refrain from eating' (fast (v)) and 'rapid, quick.' * * * "
* orotund (adj; Did You Know?: "Latin or- means 'mouth' "
(iii) Latin-English dictionary:
* ōs (noun neuter): "mouth"   (The bar over o indicates a long vowel.  The "ōr-" appears in many inflections of ōs; see table.)
(iv) YAMASHITA Sadakane 山下 定包

山下 定包: "滝田城主神余光弘(ジンヨミツヒロ) の家臣。光弘を滅ぼして領地を奪い、のちに義実に滅ぼされた。"
https://www.city.tateyama.chiba. ... hita/yamashita.html

my rough translation: was retainer/ vassal 家臣 to 神余 光弘 (owner of 滝田城) but kill the latter and took the territory -- but was later のちに killed by 義実.

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