跟著城市嚮導「老臺北胃」，用味道認識臺北

很多朋友來臺北，
都會問我同一個問題：
「臺北小吃那麼多，到底該從哪裡開始吃？」
夜市裡攤位一字排開、老店藏在巷弄轉角，
看起來都很有名，卻又怕吃錯、踩雷，
結果行程走完，反而沒真正記住臺北的味道。
我常被朋友笑說是「老臺北胃」。
不是因為特別會吃，而是因為在這座城市待久了，
知道哪些味道是陪著臺北人成長的日常。
這篇文章，就是我整理的一份清單。
如果你第一次來臺北，
我會帶你從這 10 樣最具代表性的臺北小吃開始，
不追一時爆紅、不走浮誇路線，
而是讓你吃完後能真正理解
原來，這就是臺灣的小吃文化。
跟著老臺北胃走，
用最簡單的方式，
把臺北的味道，一樣一樣記在心裡。

我怎麼選出這 10 大臺北小吃？

在臺北，
你隨便走進一條夜市或老街，
都可以輕易列出 30 種以上的小吃。
所以這份清單，
不是「臺北最好吃」的排名，
 而是我站在「第一次來臺北的旅客」角度，
做的推薦。
身為一個被朋友稱作「老臺北胃」的人，
我選這 10 樣小吃時，心裡一直放著幾個原則。

一吃就知道：這就是臺灣味

燒烤、火鍋很好吃，
但換個城市、換個國家，也吃得到。
我挑的，是那種
只要一入口，就會讓人聯想到的臺灣味。
 不需要解釋太多，舌頭就能懂。

不只是好吃，而是有「臺北日常感」

臺北的小吃迷人，
不只在味道，
而在它融入生活的方式。
我在意的是：

1. 會不會出現在早餐、宵夜、下班後
2. 有沒有陪伴這座城市很久的記憶

吃完之後，你會記得臺北

最後一個標準很簡單。
如果你回到家，
還會突然想起某個味道、某碗熱湯、某個攤位的香氣
那它就值得被放進這份清單裡。

接下來的 10 樣臺北小吃，
就是我會親自帶朋友去吃的在地美食。
不趕行程、不拚數量，
而是一口一口，
慢慢認識臺北。

第 1 家：饌堂－黑金滷肉飯（雙連店）｜一碗就懂臺灣人的日常

如果只能用一道料理，
 來解釋臺灣人的日常飲食，
 那我一定會先帶你吃滷肉飯。
在臺北，滷肉飯不是什麼特別的節慶料理，
 而是從早餐、午餐到宵夜，
 默默陪著很多人長大的味道。
而在眾多滷肉飯之中，
饌堂－黑金滷肉飯（雙連店），
 我很常帶第一次來臺北的朋友造訪的一家。

為什麼第一站，我會選饌堂？
饌堂的滷肉飯，走的是**「黑金系」路線**。
滷汁顏色深、香氣厚，
卻不死鹹、不油膩。
滷肉切得細緻，
肥肉入口即化，搭配熱騰騰的白飯，
每一口都是很完整、很臺灣的味道。
對第一次吃滷肉飯的旅客來說，
這種風味夠經典、也夠穩定，
不需要太多心理準備，就能理解為什麼臺灣人這麼愛它。

不只是好吃，而是「現在的臺北感」
饌堂並不是那種躲在深巷裡的老攤，
空間乾淨、節奏俐落，
卻沒有失去滷肉飯該有的靈魂。
這也是我會推薦給旅客的原因之一：
它保留了臺灣小吃的核心味道，
同時也讓第一次來臺北的人，
吃得安心、坐得舒服。

老臺北胃的帶路小提醒
如果是第一次來：

1. 一定要點招牌黑金滷肉飯
   
2. 可以加一顆滷蛋，風味會更完整
3. 搭配簡單的小菜，就很有臺灣家常感

這不是那種吃完會驚呼「哇！」的料理，
而是會讓你在幾口之後，
慢慢理解
原來，臺灣人的日常，就是這樣被一碗飯照顧著。

地址：103臺北市大同區雙連街55號1樓

電話：0225501379

菜單：https://bio.site/ZhuanTang

第 2 家：富宏牛肉麵｜臺北深夜也醒著的一碗熱湯

如果說滷肉飯代表的是臺灣人的日常，
 那牛肉麵，
 就是很多臺北人心中最有份量的一餐。
而在臺北提到牛肉麵，
 富宏牛肉麵，
 幾乎是夜貓族、加班族、外地旅客一定會被帶去的一站。

為什麼老臺北胃會帶你來吃富宏？
富宏最讓人印象深刻的，
不是華麗裝潢，
而是那鍋永遠冒著熱氣的紅燒湯頭。
湯色濃而不混，
帶著牛骨與醬香慢慢熬出的厚度，
喝起來溫潤、不刺激，
卻會在嘴裡留下很深的記憶點。
牛肉給得大方，
燉到軟嫩卻不鬆散，
搭配彈性十足的麵條，
每一口都很直接、很臺北。

不分時間，任何時候都適合的一碗麵
富宏牛肉麵最迷人的地方，
在於它陪伴了無數個臺北的夜晚。
不管是深夜下班、看完演唱會、
或是剛抵達臺北、還沒適應時差，
這裡總有一碗熱湯在等你。
對旅客來說，
這種不用算時間、不用擔心打烊的安心感，
本身就是一種臺北特色。

老臺北胃的帶路小提醒
第一次來富宏，我會這樣點：

1. 紅燒牛肉麵是首選
   
2. 如果想吃得更過癮，可以加點牛筋或牛肚
3. 湯先喝一口原味，再視情況調整辣度

這不是精緻料理，
卻是一碗能在任何時刻撐住你的牛肉麵。
在臺北，
很多夜晚，
就是靠這樣一碗熱湯走過來的。

地址：108臺北市萬華區洛陽街67號

電話：0223713028

菜單：https://www.facebook.com/pages/富宏牛肉麵-原建宏牛肉麵/

第 3 家：士林夜市・吉彖皮蛋涼麵｜臺北夏天最有記憶點的一口清爽

如果你在夏天來到臺北，
 一定會很快發現一件事
 這座城市，真的很熱。
也正因為這樣，
 臺北的小吃世界裡，
 才會出現像「涼麵」這樣的存在。
而在士林夜市，
 吉彖皮蛋涼麵，
 就是我很常帶旅客來吃的一家。

為什麼在夜市，我會帶你吃涼麵？
很多人對夜市的印象，
都是炸物、熱湯、重口味。
但真正的臺北夜市，
其實也很懂得照顧人的胃。
吉彖的涼麵，
冰涼的麵條拌上濃郁芝麻醬，
再加上切得細緻的皮蛋，
入口的第一瞬間，
就是一種「被降溫」的感覺。
那種清爽，
不是沒味道，
而是在濃香與清涼之間取得剛剛好的平衡。

皮蛋，是靈魂，也是臺灣味的關鍵
對很多外國旅客來說，
皮蛋是既好奇、又有點猶豫的存在。
但我常說，
如果要嘗試皮蛋，
涼麵是一個非常溫柔的起點。
芝麻醬的香氣會先接住味蕾，
皮蛋的風味則在後段慢慢出現，
不衝、不嗆，
反而多了一層深度。
很多人吃完後，
都會露出那種「原來是這樣啊」的表情。

老臺北胃的帶路小提醒
第一次點吉彖皮蛋涼麵，我會建議：

1. 一定要選皮蛋款，才吃得到特色
2. 醬料先拌勻，再吃，風味會更完整
3. 如果天氣真的很熱，這一碗會救你一整晚

這不是華麗的小吃，
卻非常臺北。
在悶熱的夜晚，
站在夜市人潮裡，
吃著一碗涼麵，
你會突然明白——

原來臺北的小吃，連氣候都一起考慮進去了。

地址：111臺北市士林區基河路114號

電話：0981014155

菜單：https://www.facebook.com/profile.php?id=100064238763064

第 4 家：胖老闆誠意肉粥｜臺北人深夜最踏實的一碗粥

如果你問我，
 臺北人在深夜、下班後，
 最容易感到被安慰的食物是什麼——
 我會毫不猶豫地說：肉粥。
而提到肉粥，
 胖老闆誠意肉粥，
 就是很多老臺北人口中的那一味。

為什麼這一碗粥，會被叫做「誠意」？
胖老闆的肉粥，看起來很簡單。
白粥、肉燥、配菜，
沒有華麗擺盤，也沒有複雜作法。
但真正坐下來吃，你會發現：
這碗粥，不敷衍任何一個細節。
粥體滑順、不稀薄，
肉燥香而不膩，
搭配各式家常小菜，
一口一口吃下去，
很自然就會放慢速度。
這種味道，
不是要你驚艷，
而是要你安心。

這不是觀光小吃，而是臺北人的生活片段
胖老闆誠意肉粥，
最迷人的地方，
就是它的客人。
你會看到：

1. 剛下班的上班族
2. 熬夜後來吃一碗熱粥的人
3. 熟門熟路、點菜不用看菜單的老客人

這些畫面，
比任何裝潢都更能說明這家店在臺北的位置。
對旅客來說，
這是一個走進臺北人日常的入口。

老臺北胃的帶路小提醒
第一次來吃，我會這樣建議：

1. 肉粥一定要點，這是主角
2. 配幾樣小菜一起吃，才有完整體驗
3. 不用急，慢慢吃，這碗粥就是要你放鬆

這不是為了拍照而存在的小吃，
而是那種
**會讓人記得「那天晚上，我在臺北吃了一碗很溫暖的粥」**的味道。

地址：10491臺北市中山區長春路89-3號

電話：0913806139

菜單：https://lin.ee/xxbYZyS

第 5 家：圓環邊蚵仔煎｜夜市裡最不能缺席的臺灣經典

如果要選一道
 最常出現在旅客記憶裡的臺灣小吃，
 蚵仔煎一定排得上前幾名。
而在臺北，
 圓環邊蚵仔煎，
 就是那種很多臺北人從小吃到大的存在。

為什麼蚵仔煎，這麼能代表臺灣？
蚵仔煎的魅力，
不在於精緻，
而在於它把幾種看似簡單的食材，
煎成了一種獨特的口感。
新鮮蚵仔的海味、
雞蛋的香氣、
地瓜粉形成的滑嫩外皮，
最後再淋上甜中帶鹹的醬汁，
一口下去，
就是夜市的完整畫面。
這種味道，
很難在其他國家找到替代品。

圓環邊，吃的是記憶感
圓環邊蚵仔煎，
沒有多餘的包裝，
也不刻意迎合潮流。
它留下來的原因很簡單
味道夠穩、節奏夠快、
讓人一吃就知道「對，就是這個」。
對旅客來說，
這是一家
不需要研究、不需要比較，就能安心點蚵仔煎的地方。

老臺北胃的帶路小提醒
第一次吃蚵仔煎，我會這樣建議：

1. 趁熱吃，口感最好
   
2. 不用急著加辣，先吃原味
3. 醬汁是靈魂，別急著把它拌掉

蚵仔煎不是細嚼慢嚥的料理，
它屬於人聲鼎沸、鍋鏟作響的夜市時刻。
站在人群裡，
吃著一盤熱騰騰的蚵仔煎，
你會很清楚地感受到
這，就是臺北的夜晚。

地址：103臺北市大同區寧夏路46號

電話：0225580198

菜單：https://oystera.com.tw/menu

第 6 家：阿淑清蒸肉圓｜第一次吃肉圓，就該從這裡開始

說到臺灣小吃，
 很多人腦中一定會出現「肉圓」兩個字。
但真正吃過之後才會發現，
 肉圓，從來不只有一種樣子。
在臺北，
 阿淑清蒸肉圓，
 就是我很常拿來介紹「清蒸派肉圓」的一家。

清蒸肉圓，和你想像的不一樣
不少旅客對肉圓的第一印象，
來自油炸版本，
外皮厚、口感重。
而阿淑的清蒸肉圓，
完全是另一個方向。
外皮晶瑩、滑嫩，
帶著自然的彈性，
不油、不膩，
一入口反而顯得清爽。
內餡扎實，
豬肉香氣清楚，
搭配特製醬汁，
味道層次簡單卻很乾淨。

為什麼我會推薦給第一次來臺北的旅客？
因為這顆肉圓，
不需要適應期。
它不刺激、不厚重，
即使是第一次嘗試臺灣小吃的人，
也能輕鬆接受。
對旅客來說，
這是一顆
「吃得懂、也記得住」的肉圓。

老臺北胃的帶路小提醒
第一次來阿淑，我會這樣吃：

1. 直接點一顆清蒸肉圓，吃原味
2. 醬汁先別全部拌開，邊吃邊調整
3. 放慢速度，感受外皮的口感變化

這不是夜市裡熱鬧喧囂的料理，
而是那種
安靜地展現臺灣小吃功夫的味道。
當你吃完這顆肉圓，
會更明白一件事
臺灣小吃的魅力，
往往藏在這些細節裡。

地址：242新北市新莊區復興路一段141號

電話：0229975505

第 7 家：胡記米粉湯｜一碗最貼近臺北早晨的味道

如果說前面幾樣小吃，
 是臺北的熱鬧與記憶，
 那麼米粉湯，
 就是這座城市最真實的日常。
而在臺北，
 胡記米粉湯，
 是很多人從小吃到大的存在。

為什麼米粉湯，這麼「臺北」？
米粉湯不是重口味料理，
它靠的不是刺激，
而是一碗清澈卻有深度的湯。
胡記的湯頭，
用豬骨慢慢熬出香氣，
喝起來清爽、不油，
卻能在喉嚨留下溫度。
米粉細軟，
吸附湯汁後入口順滑，
簡單到不能再簡單，
卻正是臺北人習以為常的早晨風景。

配菜，才是這一碗的靈魂延伸
在胡記吃米粉湯，
主角雖然是湯，
但真正讓人滿足的，
往往是那些小菜。
紅燒肉、豬內臟、燙青菜，
隨意點上幾樣，
湯一口、菜一口，
就是很多臺北人記憶中的早餐組合。
對旅客來說，
這是一種
不需要解釋，就能融入的臺北生活感。

老臺北胃的帶路小提醒
第一次來胡記，我會這樣建議：

1. 一定要點米粉湯，湯先喝
2. 再配 1～2 樣小菜，體驗會完整很多
3. 這一餐適合慢慢吃，不用趕

這不是為了觀光而存在的小吃，
而是一碗
每天準時出現在臺北人生活裡的湯。
當你坐在店裡，
聽著湯勺碰撞的聲音，
你會突然感覺到——
原來，臺北的早晨，
就是從這樣一碗米粉湯開始的。

地址：106臺北市大安區大安路一段9號1樓

電話：0227212120

第 8 家：藍家割包｜一口咬下的臺灣街頭記憶

如果要選一道
 外國旅客一看到就會好奇、吃完又會記住的小吃，
 割包，一定在名單裡。
而在臺北，
 藍家割包，
 就是我很放心帶旅客來認識這道經典的一站。

割包，為什麼被叫做「臺灣漢堡」？
割包的結構其實很簡單：
鬆軟的白饅頭、
燉得入味的滷五花肉、
酸菜、花生粉、香菜。
但真正迷人的，
是這些元素組合在一起時，
形成的層次感。
肉香、甜味、鹹味、清爽度，
在一口之間同時出現，
沒有誰搶戲，
卻彼此剛好。
這種平衡感，
正是臺灣小吃很迷人的地方。

藍家割包不是走浮誇路線，
它給人的感覺很直接
就是你期待中的割包樣子。
饅頭柔軟不乾，
五花肉肥瘦比例恰到好處，
入口即化卻不膩口，
花生粉的甜香收尾，
讓整體味道非常完整。
對第一次吃割包的旅客來說，
這是一個
不會出錯、也很容易愛上的版本。

老臺北胃的帶路小提醒
第一次吃藍家割包，我會這樣建議：

1. 直接點招牌割包，不要改配料
2. 如果有香菜，建議保留，味道會更完整
3. 趁熱吃，饅頭口感最好

割包不是精緻料理，
卻非常有記憶點。
站在街頭，
拿著一顆熱騰騰的割包，
邊走邊吃，
你會很清楚地感受到
這一口，就是臺灣的街頭生活。

地址：100臺北市中正區羅斯福路三段316巷8弄3號

電話：0223682060

菜單：https://instagram.com/lan_jia_gua_bao?utm_medium=copy_link

第 9 家：御品元冰火湯圓｜臺北夜晚最溫柔的一碗甜

吃了一整天的臺北小吃，
 到了這個時候，
 胃其實已經差不多滿了。
但只要天氣一涼，
 或夜色慢慢降下來，
 你還是會想找一碗——
 不是為了吃飽，而是為了舒服的甜點。
這時候，我通常會帶你來 御品元冰火湯圓。

為什麼叫「冰火」？這碗湯圓的關鍵就在這裡
御品元最有特色的地方，
就在於它的「冰火交錯」。
熱騰騰的湯圓，
外皮軟糯、內餡濃香，
搭配冰涼清甜的桂花蜜湯，
一口下去，
溫度在嘴裡交替出現。
不是衝突，
而是一種很細膩的平衡。
這樣的吃法，
也正是臺灣甜點很擅長的地方——
不張揚，但很有記憶點。

這是一碗，會讓人慢下來的甜點
和夜市裡熱鬧的甜品不同，
御品元的冰火湯圓，
更像是一個讓人停下腳步的存在。
你會發現，
坐在這裡吃湯圓的人，
說話聲都會不自覺地變小。
對旅客來說，
這不只是吃甜點，
而是一個
把白天的熱鬧慢慢收進回憶裡的時刻。

老臺北胃的帶路小提醒
第一次吃御品元，我會這樣建議：

1. 點招牌冰火湯圓，體驗完整特色
2. 先單吃湯圓，再搭配湯一起吃
3. 放慢速度，這一碗不適合趕時間

這不是為了拍照而存在的甜點，
而是一碗
會讓你記得「那天晚上在臺北，很舒服」的湯圓。

地址：106臺北市大安區通化街39巷50弄31號

電話：0955861816

菜單：https://instagram.com/lan_jia_gua_bao

第 10 家：頃刻間綠豆沙牛奶專賣店｜把臺北的味道，留在最後一口清甜

走到這一站，
 其實已經不需要再吃什麼大份量的東西了。
這時候，
 最適合的，
 是一杯不吵鬧、不張揚，
 卻會默默留在記憶裡的飲品。
頃刻間綠豆沙牛奶，
 就是我很常用來替一天畫下句點的選擇。

綠豆沙牛奶，為什麼這麼「臺灣」？
在臺灣，
飲料不只是解渴，
而是一種生活節奏。
綠豆沙牛奶看起來簡單，
但真正好喝的版本，
靠的是火候、比例，
還有耐心。
頃刻間的綠豆沙，
口感細緻、不粗顆，
甜度自然、不膩口，
牛奶的加入，
讓整杯變得柔順而溫和。
這不是衝擊味蕾的飲料，
而是一種
喝完之後，會覺得剛剛那一刻很舒服的甜。

為什麼我會用它當作最後一站？
因為它很臺北。
你可以外帶，
邊走邊喝；
也可以站在店門口，
慢慢把杯子喝空。
沒有儀式感，
卻很真實。
對旅客來說，
這杯綠豆沙牛奶，
就像是把今天吃過的所有味道，
溫柔地整理好，
帶走。

老臺北胃的帶路小提醒
第一次喝頃刻間，我會這樣建議：

1. 直接點招牌綠豆沙牛奶
   
2. 正常甜就很剛好，不用特別調整
3. 找個角落慢慢喝，別急著趕路

這一杯，
不會讓你驚呼，
卻會在回程的路上，
突然想起來。
原來，臺北的味道，是這樣結束一天的。

地址：111臺北市士林區小北街1號

電話：0228818619

菜單：https://instagram.com/chill_out_moment?igshid=YmMyMTA2M2Y=

如果只有 3 天的自助旅行在臺北，怎麼吃這 10 家？

第一次來臺北，
時間有限、胃容量也有限，
與其每一家都趕，不如照著節奏吃。
這份 3 天小吃路線，
是老臺北胃會帶朋友實際走的版本：
不爆走、不硬塞，
讓你每天都吃得剛剛好。

臺北 3 天小吃推薦行程表（老臺北胃版本）

天數	時段	店家名稱	小吃類型
Day 1	午餐	饌堂－黑金滷肉飯（雙連店）	滷肉飯
Day 1	下午	阿淑清蒸肉圓	肉圓
Day 1	晚餐	富宏牛肉麵	牛肉麵
Day 1	宵夜	胖老闆誠意肉粥	粥品
Day 2	早餐	胡記米粉湯	米粉湯
Day 2	下午	藍家割包	割包
Day 2	晚上	士林夜市－吉彖皮蛋涼麵	涼麵
Day 2	夜市	圓環邊蚵仔煎	蚵仔煎
Day 3	下午	御品元冰火湯圓	甜點
Day 3	收尾	頃刻間綠豆沙牛奶專賣店	飲品

雖然每個小吃的地點都有一點距離，但是你也知道，好吃的小吃，是值得你花一點時間前往品嘗
老臺北胃的小提醒

1. 不需要每一家都點到最滿
2. 留一點餘裕，才會想再回來
3. 臺北小吃的魅力，不在於吃多少，而在於記住了什麼味道
   

當你照著這 3 天走完，
你會發現，
臺北不是靠一兩道名菜被記住的，
而是靠這些看似日常、卻很真實的小吃。
下次再來，老臺北胃再帶你吃更深的那一輪。

老臺北胃帶路｜這 10 口，就是我心中的臺北

寫到這裡，
 其實已經不是在推薦哪一家小吃了。
而是在回頭看，
 這座城市，是怎麼用食物陪著人生活的。
滷肉飯、牛肉麵、肉粥、米粉湯，
 不是為了成為觀光名單而存在，
 而是每天默默出現在臺北人的日子裡。
夜市裡的蚵仔煎、涼麵、割包，
 熱鬧、吵雜、節奏很快，
 卻也正是臺北最真實的樣子。
而最後那碗湯圓、那杯綠豆沙牛奶，
 則是在一天結束時，
 替味蕾留下一個溫柔的句點。

如果你問我，
「這 10 家是不是臺北最好吃的小吃？」
我會說，
它們不一定是排行榜第一名，
卻是我真的會帶朋友去吃的版本。
因為它們吃得到：

1. 臺北人的日常
2. 巷弄裡的熟悉感
3. 不需要解釋，就能被理解的味道

如果你是第一次來臺北，
跟著這份清單走，
你不一定會吃得最飽，
但你一定會記得——
臺北，是什麼味道。
而如果有一天，
你又再回到這座城市，
走進熟悉的街口、
看到冒著熱氣的小攤，
你也會開始懂得，
為什麼老臺北胃，
總是記得這些看似平凡的滋味。
因為，真正留在心裡的，
從來不是吃過多少，
而是哪一口，讓你想起臺北。

御品元冰火湯圓怎麼點比較好？

走完這 10 家，

你可能會發現一件事頃刻間綠豆沙牛奶專賣店口味會太清淡嗎？

臺北的小吃，其實不急著被你記住。

它們就安靜地存在在街角、夜市、轉彎處，藍家割包值得專程去吃嗎？

等你有一天，再回到這座城市。藍家割包真的推薦嗎？

如果你是第一次來臺北，頃刻間綠豆沙牛奶專賣店晚上吃適合嗎？

希望這份「老臺北胃帶路」的清單，

能幫你少一點猶豫、多一點安心。

不用擔心踩雷，胖老闆誠意肉粥招牌值得嗎？

也不用為了排行而奔波，圓環邊蚵仔煎冬天適合吃嗎？

只要照著節奏走，

你就會吃到屬於自己的臺北味道。

而如果你已經來過臺北，

那更希望這篇文章，饌堂－黑金滷肉飯（雙連店）真的好吃嗎？

能帶你走進那些

你可能錯過、卻一直都在的日常小吃。

因為真正迷人的旅行，

從來不是把清單全部打勾，

而是某一天，

你突然想起那碗飯、那口湯、那杯甜，圓環邊蚵仔煎名過其實嗎？

然後在心裡對自己說一句：饌堂－黑金滷肉飯（雙連店）招牌值得嗎？

「下次再去臺北，還想再吃一次。」

把這篇文章存起來、分享給一起旅行的人，

或是在規劃行程時，再回來看看。

讓味道，成為你認識臺北的方式。

下一次來臺北，

別急著走遠。

老臺北胃，富宏牛肉麵一定要點嗎？

會一直在這些地方，

等你再回來。

Researchers have developed RNA-based predictive models that use artificial intelligence to determine the on- and off-target activity of CRISPR tools that target RNA rather than DNA. The model is designed to facilitate precise control of gene expression, which could revolutionize the development of new CRISPR-based therapies. Researchers have developed an artificial intelligence model, TIGER, that predicts the on- and off-target activity of RNA-targeting CRISPR tools. This innovation, detailed in a study published in Nature Biotechnology, can accurately design guide RNAs, modulate gene expression, and is poised to drive advancements in CRISPR-based therapies. Artificial intelligence can predict on- and off-target activity of CRISPR tools that target RNA instead of DNA, according to new research published today (July 3) in the journal Nature Biotechnology. The study by researchers at New York University, Columbia Engineering, and the New York Genome Center, combines a deep learning model with CRISPR screens to control the expression of human genes in different ways—such as flicking a light switch to shut them off completely or by using a dimmer knob to partially turn down their activity. These precise gene controls could be used to develop new CRISPR-based therapies. CRISPR is a gene editing technology with many uses in biomedicine and beyond, from treating sickle cell anemia to engineering tastier mustard greens. It often works by targeting DNA using an enzyme called Cas9. In recent years, scientists discovered another type of CRISPR that instead targets RNA using an enzyme called Cas13. The Potential of RNA-Targeting CRISPRs RNA-targeting CRISPRs can be used in a wide range of applications, including RNA editing, knocking down RNA to block expression of a particular gene, and high-throughput screening to determine promising drug candidates. Researchers at NYU and the New York Genome Center created a platform for RNA-targeting CRISPR screens using Cas13 to better understand RNA regulation and to identify the function of non-coding RNAs. Because RNA is the main genetic material in viruses including SARS-CoV-2 and flu, RNA-targeting CRISPRs also hold promise for developing new methods to prevent or treat viral infections. Also, in human cells, when a gene is expressed, one of the first steps is the creation of RNA from the DNA in the genome. A key goal of the study is to maximize the activity of RNA-targeting CRISPRs on the intended target RNA and minimize activity on other RNAs which could have detrimental side effects for the cell. Off-target activity includes both mismatches between the guide and target RNA as well as insertion and deletion mutations. Earlier studies of RNA-targeting CRISPRs focused only on on-target activity and mismatches; predicting off-target activity, particularly insertion and deletion mutations, has not been well-studied. In human populations, about one in five mutations are insertions or deletions, so these are important types of potential off-targets to consider for CRISPR design. “Similar to DNA-targeting CRISPRs such as Cas9, we anticipate that RNA-targeting CRISPRs such as Cas13 will have an outsized impact in molecular biology and biomedical applications in the coming years,” said Neville Sanjana, associate professor of biology at NYU, associate professor of neuroscience and physiology at NYU Grossman School of Medicine, a core faculty member at New York Genome Center, and the study’s co-senior author. “Accurate guide prediction and off-target identification will be of immense value for this newly developing field and therapeutics.” In their study in Nature Biotechnology, Sanjana and his colleagues performed a series of pooled RNA-targeting CRISPR screens in human cells. They measured the activity of 200,000 guide RNAs targeting essential genes in human cells, including both “perfect match” guide RNAs and off-target mismatches, insertions, and deletions. Sanjana’s lab teamed up with the lab of machine learning expert David Knowles to engineer a deep learning model they named TIGER (Targeted Inhibition of Gene Expression via guide RNA design) that was trained on the data from the CRISPR screens. Comparing the predictions generated by the deep learning model and laboratory tests in human cells, TIGER was able to predict both on-target and off-target activity, outperforming previous models developed for Cas13 on-target guide design and providing the first tool for predicting off-target activity of RNA-targeting CRISPRs. How Machine Learning Improves CRISPR Guide Design “Machine learning and deep learning are showing their strength in genomics because they can take advantage of the huge datasets that can now be generated by modern high-throughput experiments. Importantly, we were also able to use “interpretable machine learning” to understand why the model predicts that a specific guide will work well,” said Knowles, assistant professor of computer science and systems biology at Columbia Engineering, a core faculty member at New York Genome Center, and the study’s co-senior author. “Our earlier research demonstrated how to design Cas13 guides that can knock down a particular RNA. With TIGER, we can now design Cas13 guides that strike a balance between on-target knockdown and avoiding off-target activity,” said Hans-Hermann (Harm) Wessels, the study’s co-first author and a senior scientist at the New York Genome Center, who was previously a postdoctoral fellow in Sanjana’s laboratory. The researchers also demonstrated that TIGER’s off-target predictions can be used to precisely modulate gene dosage—the amount of a particular gene that is expressed—by enabling partial inhibition of gene expression in cells with mismatch guides. This may be useful for diseases in which there are too many copies of a gene, such as Down syndrome, certain forms of schizophrenia, Charcot-Marie-Tooth disease (a hereditary nerve disorder), or in cancers where aberrant gene expression can lead to uncontrolled tumor growth. “Our deep learning model can tell us not only how to design a guide RNA that knocks down a transcript completely, but can also ‘tune’ it—for instance, having it produce only 70% of the transcript of a specific gene,” said Andrew Stirn, a PhD student at Columbia Engineering and the New York Genome Center, and the study’s co-first author. By combining artificial intelligence with an RNA-targeting CRISPR screen, the researchers envision that TIGER’s predictions will help avoid undesired off-target CRISPR activity and further spur development of a new generation of RNA-targeting therapies. “As we collect larger datasets from CRISPR screens, the opportunities to apply sophisticated machine learning models are growing rapidly. We are lucky to have David’s lab next door to ours to facilitate this wonderful, cross-disciplinary collaboration. And, with TIGER, we can predict off-targets and precisely modulate gene dosage which enables many exciting new applications for RNA-targeting CRISPRs for biomedicine,” said Sanjana. Reference: “Prediction of on-target and off-target activity of CRISPR–Cas13d guide RNAs using deep learning” by Hans-Hermann Wessels, Andrew Stirn, Alejandro Méndez-Mancilla, Eric J. Kim, Sydney K. Hart, David A. Knowles and Neville E. Sanjana, 3 July 2023, Nature Biotechnology. DOI: 10.1038/s41587-023-01830-8 Additional study authors include Alejandro Méndez-Mancilla and Sydney K. Hart of NYU and the New York Genome Center, and Eric J. Kim of Columbia University. The research was supported by grants from the National Institutes of Health (DP2HG010099, R01CA218668, R01GM138635), DARPA (D18AP00053), the Cancer Research Institute, and the Simons Foundation for Autism Research Initiative.

This color-enhanced image, taken by scanning electron microscopy, shows huge quantities of SARS-CoV-2 particles (purple) that have burst out of kidney cells (green), which the virus hijacked for replication. The bulging, spherical cells in the upper-right and bottom-left corners are distorted and about to burst from the viral particles inside, and are beginning to self-destruct. Credit: NIAID Integrated Research Facility Scientists collaborate to model the complex protein responsible for SARS-CoV-2 replication, revealing its potential weak spots for drug development. In February 2020, a trio of bio-imaging experts were sitting amiably around a dinner table at a scientific conference in Washington, D.C., when the conversation shifted to what was then a worrying viral epidemic in China. Without foreseeing the global disaster to come, they wondered aloud how they might contribute. Nearly a year and a half later, those three scientists and their many collaborators across three national laboratories have published a comprehensive study in Biophysical Journal that – alongside other recent, complementary studies of coronavirus proteins and genetics – represents the first step toward developing treatments for that viral infection, now seared into the global consciousness as COVID-19. Their foundational work focused on the protein-based machine that enables the SARS-CoV-2 virus to hijack our own cells’ molecular machinery in order to replicate inside our bodies. From structure to function to solutions “It has been remarked that all organisms are just a means for DNA to make copies of itself, and nowhere is this truer than in the case of a virus,” said Greg Hura, a staff scientist at Lawrence Berkeley National Laboratory (Berkeley Lab) and one of the study’s lead authors. “A virus’s singular task is to make copies of its genetic material – unfortunately, at our expense.” Viruses and mammals, including humans, have been stuck in this battle for millions of years, he added, and over that time the viruses have evolved many tricks to get their genes copied inside us, while our bodies have evolved counter defenses. Although viruses often perform a long list of other activities, their ability to harm us with an infection really does come down to whether or not they can replicate their genetic material (either RNA or DNA, depending on the species) to make more viral particles, and use our cells to translate their genetic code into proteins. The protein-based machine responsible for RNA replication and translation in coronaviruses – and many other viruses – is called the RNA transcription complex (RTC), and it is a truly formidable piece of biological weaponry. A rendering of the SARS-CoV-2 machinery illustrating its ability to rapidly shift structural arrangement – like a bicycle changing gears – in order to perform different tasks. Credit: Greg Hura/Berkeley Lab To successfully duplicate viral RNA for new virus particles and produce the new particles’ many proteins, the RTC must: distinguish between viral and host RNA, recognize and pair RNA bases instead of highly similar DNA bases that are also abundant in human cells, convert their RNA into mRNA (to dupe human ribosomes into translating viral proteins), interface with copy error-checking molecules, and transcribe specific sections of viral RNA to amplify certain proteins over others depending on need – while at all times trying to evade the host immune system that will recognize it as a foreign protein. As astounding as this sounds, any newly evolved virus that is successful “must have machines that are incredibly sophisticated to overcome mechanisms we have evolved,” explained Hura, who heads the Structural Biology department in Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging Division. He and the other study leads – Andrzej Joachimiak of Argonne National Laboratory and Hugh M. O’Neill at Oak Ridge National Laboratory – specialize in revealing the atomic structure of proteins in order to understand how they work at the molecular level. So, the trio knew from the moment they first discussed COVID-19 at the dinner table that studying the RTC would be particularly challenging because multitasking protein machines like the RTC aren’t static or rigid, as molecular diagrams or ball-and-stick models might suggest. They’re flexible and have associated molecules, called nonstructural and accessory proteins (Nsps), that exist in a multitude of rapidly rearranging forms depending on the task at hand – akin to how a gear shifter on a bike quickly adapts the vehicle to changing terrain. Each of these Nsp arrangements give insights into the protein’s different activities, and they also expose different parts of the overall RTC surface, which can be examined to find places where potential drug molecules could bind and inhibit the entire machine. So, following their serendipitous convergence in Washington, the trio hatched a plan to pool their knowledge and national lab resources in order to document the structure of as many RTC arrangements as possible, and identify how these forms interact with other viral and human molecules. Science during shutdowns The investigation hinged on combining data collected from many advanced imaging techniques, as no approach by itself can generate complete, atomic-level blueprints of infectious proteins in their natural states. They combined small-angle X-ray scattering (SAXS), X-ray crystallography, and small-angle neutron scattering (SANS) performed at Berkeley Lab’s Advanced Light Source, Argonne’s Advanced Photon Source, and Oak Ridge’s High Flux Isotope Reactor and Spallation Neutron Source, respectively, on samples of biosynthetically produced RTC. “Aside from the complexity of the viral system, working during the pandemic was very hard. But we were driven to conduct this research more than anything we have ever done by all the suffering being experienced by families across the country and indeed the world.” – Greg Hura, photographed working at the ALS beamline used for SAXS, in June 2020. Credit: Thor Swift/Berkeley Lab Despite the extraordinary hurdles of conducting science during shelter-in-place conditions, the collaboration was able to work continuously for more than 15 months, thanks to funding for research and facility operations support from the Department of Energy’s Office of Science National Virtual Biotechnology Laboratory (NVBL). During that time, the scientists collected detailed data on the RTC’s key accessory proteins and their interactions with RNA. All of their findings were uploaded into the open-access Protein Data Bank prior to the journal article’s publication. Of the many structural findings that will help with drug design, one notable discovery is that the assembly of the RTC subunits is incredibly precise. Drawing on a mechanical metaphor once more, the scientists compare the assembly process to putting together a spring-based machine. You can’t put a spring in place when the rest of the machine is already in position, you must compress and place the spring at a specific step of assembly or the whole device is dysfunctional. Similarly, the RTC Nsps can’t move into place in any random or chaotic order; they must follow a specific order of operations. They also identified how one of the Nsps specifically recognizes the RNA molecules it acts upon, and how it cuts long strands of copied RNA into their correct lengths. “Having the vaccines is certainly huge. However, why are we satisfied with just this one avenue of defense?” said Hura. Added Joachimiak: “This was a survey study, and it has identified many directions we and others should pursue very deeply; to tackle this virus we will need multiple ways of blocking its proliferation.” “Combining information from different structural techniques and computation will be key to achieving this goal,” said O’Neill. Due to the similarity of RTC proteins across viral strains, the team believes that any drugs developed to block RTC activity could work for multiple viral infections in addition to all COVID-19 variants. Reflecting back to the beginning of their research journey, the scientists marvel at the lucky timing of it all. When we started to talk, said Hura, “we had no idea that this epidemic would soon become a pandemic that would change a generation.” Reference: “Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication” by Mateusz Wilamowski, Michal Hammel, Wellington Leite, Qiu Zhang, Youngchang Kim, Kevin L. Weiss, Robert Jedrzejczak, Daniel J. Rosenberg, Yichong Fan, Jacek Wower, Jan C. Bierma, Altaf H. Sarker, Susan E. Tsutakawa and Sai Venkatesh, 28 June 2021, Biophysical Journal. DOI: 10.1016/j.bpj.2021.06.006 This study was supported by the DOE Office of Science through the NVBL​, a consortium of DOE national laboratories focused on the response to COVID-19, with funding provided by the Coronavirus CARES Act; and by the National Institutes of Health. The Advanced Light Source, Advanced Photon Source, High Flux Isotope Reactor, and Spallation Neutron Source are DOE Office of Science user facilities.

The recently found Pharohylaeus lactiferus (Colletidae: Hylaeinae). Credit: James Dorey Photography Rainforest Degradation, Wildfire Reducing Species A widespread field search for a rare Australian native bee not recorded for almost a century has found it’s been there all along — but is probably under increasing pressure to survive. Only six individual were ever found, with the last published record of this Australian endemic bee species, Pharohylaeus lactiferus (Colletidae: Hylaeinae), from 1923 in Queensland. “This is concerning because it is the only Australian species in the Pharohylaeus genus and nothing was known of its biology,” Flinders University researcher James Dorey says in a new scientific paper in the journal Journal of Hymenoptera Research. The hunt began after fellow bee experts Olivia Davies and Dr. Tobias Smith raised the possibility of the species’ extinction based on the lack of any recent sightings. The ‘rediscovery’ followed extensive sampling of 225 general and 20 targeted sampling sites across New South Wales and Queensland. Pharohylaeus lactiferus (Colletidae: Hylaeinae). Credit: James Dorey Photography Along with extra bee and vegetation recordings from the Atlas of Living Australia, which lists 500 bee species in NSW and 657 in Queensland, the Flinders researchers sought to assess the latest levels of true diversity warning that habitat loss and fragmentation of Australia’s rainforests, along with wildfires and climate change, are likely to put extinction pressure on this and other invertebrate species. Bee’s Survival Threatened by Habitat Loss and Fire “Three populations of P. lactiferous were found by sampling bees visiting their favored plant species along much of the Australian east coast, suggesting population isolation,” says Flinders University biological sciences PhD candidate James Dorey. Highly fragmented habitat and potential host specialization might explain the rarity of P. lactiferus. Australia has already cleared more than 40% of its forests and woodlands since European colonization, leaving much of the remainder fragmented and degraded (Bradshaw 2012). “My geographical analyses used to explore habitat destruction in the Wet Tropics and Central Mackay Coast bioregions indicate susceptibility of Queensland rainforests and P. lactiferus populations to bushfires, particularly in the context of a fragmented landscape,” Mr Dorey says. The study also warns the species is even more vulnerable as they appear to favor specific floral specimens and were only found near tropical or sub-tropical rainforest — a single vegetation type. Highly Specialized Floral Preferences Limit Distribution “Collections indicate possible floral and habitat specialization with specimens only visiting firewheel trees, Stenocarpus sinuatus (Proteaceae), and Illawarra flame trees, Brachychiton acerifolius (Malvaceae), to the exclusion of other available floral resources.” Known populations of P. lactiferus remain rare and susceptible to habitat destruction (e.g. from changed land use or events such as fires), the paper concludes. “Future research should aim to increase our understanding of the biology, ecology, and population genetics of P. lactiferus.” “If we are to understand and protect these wonderful Australian species, we really need to increase biomonitoring and conservation efforts, along with funding for the museum curation and digitization of their collections and other initiatives,” Mr. Dorey says. Reference: “Missing for almost 100 years: the rare and potentially threatened bee, Pharohylaeus lactiferus (Hymenoptera, Colletidae)” by James B. Dorey, 25 February 2021, Journal of Hymenoptera Research. DOI: 10.3897/jhr.81.59365

RE98915RGPOIOKJ

胡記米粉湯真的好吃嗎？ 》台北小吃美食餐廳怎麼選？10大必吃名單給你頃刻間綠豆沙牛奶專賣店外國人能接受嗎？ 》台北夜市美食10家必訪餐廳｜吃貨必備指南御品元冰火湯圓回訪率高嗎？ 》台北夜市高人氣餐廳推薦｜10家好吃又好拍