瘧原蟲青蒿素抗藥性的分子標記

青蒿素提取自傳統(tǒng)中藥青蒿（Artemisia annua），與其他藥物聯(lián)合使用可用于治療瘧疾。為監(jiān)測具有青蒿素抗性的瘧原蟲，法國巴斯德研究所的研究人員識別出“鐮刀形瘧原蟲”青蒿素抗藥性的一個主要決定因子。該寄生蟲的PF3D7＿1343700kelch propeller domain（K-13propeller）中發(fā)生的等位基因突變頻率增加與最近的抗藥性傳播有關(guān)。該發(fā)現(xiàn)除提出一個有用的分子標記外，還有助于加深對抗藥性形成的認識，并為在新型抗瘧疾藥物減少抗藥性提供思路。

論文鏈接： Ariey F，et al..A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide.To monitor the spread of artemisinin resistance，a molecular marker is urgently needed.Here，using wholegenome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia，we associate mutations in the PF3D7＿1343700kelch propeller domain（‘K13-propeller’）with artemisinin resistance in vitro and in vivo.Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent，and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia.Strong correlations between the presence of a mutant allele，in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance.K13-propeller polymorphism constitutes a useful molecular marker for largescale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.

新方法可批量制備用于表觀遺傳學(xué)研究的重組抗體

目前研究中使用的抗體大多經(jīng)過不同批次從動物體內(nèi)產(chǎn)生獲得，而每批次之間存在著較大的質(zhì)量變化，對研究工作產(chǎn)生影響。研究人員放棄通過動物進行抗體生產(chǎn)，轉(zhuǎn)而利用遺傳手段在細菌體內(nèi)制造具有高識別度的重組抗體以用于組蛋白的特定修飾。通過與市場上用動物制成的抗體相比較，這種新抗體的表現(xiàn)更佳，質(zhì)量完全不受批次時間影響。這種抗體制備方法還能開發(fā)出經(jīng)過一種以上化學(xué)修飾的抗體，可幫助破解如相鄰甲基基團或其他表觀遺傳修飾的組合是如何影響基因表達等相關(guān)問題。

論文鏈接： Hattori T，et al..Recombinant antibodies to histone post-translational modifications.

Nature Methods，2013，（10），992-995.doi：10.1038／nmeth.2605.

Abstract：Variability in the quality of antibodies to histone post-translational modifications（PTMs）is a widely recognized hindrance in epigenetics research.Here，we produced recombinant antibodies to the trimethylated lysine residues of histone H3with high specificity and affinity and no lot-to-lot variation.These recombinant antibodies performed well in common epigenetics applications，and enabled us to identify positive and negative correlations amonghistone PTMs.

促進腸道固有菌群的互利抗菌機制

人體的上皮細胞通過各種抗菌蛋白的保護，能夠與復(fù)雜的細菌群落密切共存。C-型外源凝集素RegIII蛋白家族是一類殺菌性蛋白，可限制細菌和腸上皮細胞間的直接接觸，從而促進腸道對菌群的耐受性。研究發(fā)現(xiàn)，RegIIIα（也稱為HIP／PAP）是這一蛋白家族的一員，可結(jié)合細胞膜磷脂，并通過形成六聚體低聚物孔隙使膜通透化而殺死革蘭氏陽性細菌，對革蘭氏陰性菌不起作用。該項研究能夠幫助深入了解促進固有菌群的互利抗菌機制。

論文鏈接： Mukherjee S，et al..Antibacterial membrane attack by apore-forming intestinal C-type lectin.

Nature，doi：10.1038／nature12729.Published online：20November，2013.

Abstract：Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins.C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bacteria and the intestinal epithelium and thus promote tolerance to the intestinal microbiota.RegIII lectins recognize their bacterial targets by binding peptidoglycan carbohydrate，but the mechanism by which they kill bacteria is unknown.Here we elucidate the mechanistic basis for RegIII bactericidal activity.We show that human RegIIIα （also known as HIP／PAP）binds membrane phospholipids and kills bacteria by forming a hexameric membrane-permeabilizing oligomeric pore.We derive a three-dimensional model of the RegIIIαpore by docking the RegIIIαcrystal structure into a cryo-electron microscopic map of the pore complex，and show that the model accords with experimentally determined properties of the pore.Lipopolysaccharide inhibits RegIIIαpore-forming activity，explaining why RegIIIαis bactericidal for Gram-positive but not Gram-negative bacteria.Our findings identify C-type lectins as mediators of membrane attack in the mucosal immune system，and provide detailed insight into an antibacterial mechanism that promotes mutualism with the resident microbiota.

葉酸缺乏導(dǎo)致小鼠精子DNA變化

表觀遺傳DNA改變（如DNA甲基化）會改變基因活性，但不影響DNA的序列。研究發(fā)現(xiàn)，飲食中的葉酸會影響細胞DNA甲基化水平和基因表達，給雄性小鼠終生喂食缺乏葉酸的食物，導(dǎo)致雄性小鼠精子DNA甲基化發(fā)生改變且生育能力降低。這些雄性小鼠的雄性和雌性后代產(chǎn)生發(fā)育異常的頻率都要比采用正常飲食的雄性小鼠的后代高。在一些情況下，這些小鼠會生出有顱面缺陷和脊椎畸形等發(fā)育異常的后代。目前這種表觀遺傳傳遞的機制還不清楚，造成發(fā)育缺陷的分子水平原因尚待研究。

論文鏈接： R.Lambrot，et al..Low paternal dietary folate alters the mouse sperm epigenome and is associated with negative pregnancy outcomes.

Nature Communications，2013，4（2889）.doi：10.1038／ncomms3889.

Abstract：Epidemiological studies suggest that a father’s diet can influence offspring health.A proposed mechanism for paternal transmission of environmental information is via the sperm epigenome.The epigenome includes heritable information such as DNA methylation.We hypothesize that the dietary supply of methyl donors will alter epigenetic reprogramming in sperm.Here we feed male mice either a folate-deficient or folate-sufficient diet throughout life.Paternal folate deficiency is associated with increased birth defects in the offspring，which include craniofacial and musculoskeletal malformations.Genome-wide DNA methylation analysis and the subsequent functional analysis identify differential methylation in sperm of genes implicated in development，chronic diseases such as cancer，diabetes，autism and schizophrenia.While＞300genes are differentially expressed in offspring placenta，only two correspond to genes with differential methylation in sperm.This model suggests epigenetic transmission may involve sperm histone H3methylation or DNA methylation and that adequate paternal dietary folate is essential for offspringhealth.

評估熒光蛋白的光激活效率

光控的熒光探針，是對局部進行超高分辨率顯微分析的核心。其中，熒光蛋白可以通過基因編碼，實現(xiàn)與目的蛋白的1∶1標記。所以，熒光蛋白探針特別適合于單分子計數(shù)。ICFO的科學(xué)家們對所有已知的“不可逆光控熒光蛋白”，進行了光激活效率的檢測，為蛋白的分子定量提供了相當詳細的參考框架。研究人員用爪蟾卵母細胞表達的人類甘氨酸受體作為納米模板，對多種熒光蛋白進行分析，確定了被光激活的蛋白比率。該方法理論上可以對目標蛋白進行分子定量，但仍有限制。通過對該方法參數(shù)的優(yōu)化，可以生成更適合超高分辨率分子計數(shù)的探針。

論文鏈接： Durisic N，et al..Single-molecule evaluation of fluorescent protein photoactivation efficiency using an in vivo nanotemplate.

Nature Methods，doi：10.1038／nmeth.2784.Published online：05January，2014.

Abstract：Photoswitchable fluorescent probes are central to localization-based super-resolution microscopy.Among these probes，fluorescent proteins are appealing because they are genetically encoded.Moreover，the ability to achieve a 1：1labeling ratio between the fluorescent protein and the protein of interest makes these probes attractive for quantitative single-molecule counting.The percentage of fluorescent protein that is photoactivated into a fluorescently detectable form （i.e.，the photoactivation efficiency）plays a crucial part in properly interpreting the quantitative information.It is important to characterize the photoactivation efficiency at the single-molecule level under the conditions used in super-resolution imaging.Here，we used the human glycine receptor expressed in Xenopus oocytes and stepwise photobleaching or single-molecule counting photoactivated localization microcopy（PALM）to determine the photoactivation efficiency of fluorescent proteins mEos2，mEos3.1，mEos3.2，Dendra2，mClavGR2，mMaple，PA-GFP and PA-mCherry.This analysis provides important information that must be considered when using these fluorescent proteins in quantitative super-resolution microscopy.

大鼠多基因同步敲除技術(shù)

實驗中敲除一個基因很容易實現(xiàn)，但動物的某個性狀往往由幾個基因同時控制，因此多基因同步敲除技術(shù)更為重要。不過，目前多基因同步敲除還存在技術(shù)上的障礙。我國研究人員首次利用CRISPRCas系統(tǒng)誘導(dǎo)大鼠的Tet1／Tet2／Tet3基因敲除，實現(xiàn)了效率高達100%的雙等位基因純合突變的單基因敲除和接近60%高效率的三基因同時敲除大鼠，并且證明CRISPR-Cas系統(tǒng)引入的基因修飾可通過生殖細胞傳遞到下一代。該技術(shù)可推動基因修飾大鼠成為重要的動物模型。

論文鏈接： Wei Li，et al..Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems.

Nature Biotechnology，2013，31：684-686.doi：10.1038／nbt.2652.

Abstract：CRISPRs are clustered，regularly interspaced，short palindromic repeats present in many bacteria and archaea genomes.Proteins encoded by CRISPR-associated（Cas）genes serve as guardians of the genome，which target foreign DNA at specific sites by means of small CRISPR RNA（crRNA）-guided DNA recognition and degradation.Recently，several groups described how CRISPRCas systems efficiently create site-specific gene modifications in whole organisms such as Streptococcus pneumoniae，Escherichia coli，Danio rerio（zebrafish）and mice，suggesting its potential application in the production of genetically engineered organisms，although germline transmission of the mutations remains to be shown.Here，we report the use of CRISPR-Cas systems to generate multiple gene mutations in rats in a germline-competent manner.

高粱基因組存在遺傳變異

中澳兩國研究人員合作對重要糧食飼料作物高粱進行了全基因組測序及分析。該研究通過對44株不同來源的高粱樣本，包括地方品種、改良品種和野生雜草材料，進行了全基因組重測序及分析，并首次對擬高粱進行了全基因組測序。研究發(fā)現(xiàn)，高粱與擬高粱都存在豐富的遺傳多樣性。通過比較分析，科研人員還發(fā)現(xiàn)不同的高粱品種在基因組中存在著強烈的種群結(jié)構(gòu)差異和復(fù)雜的馴化歷程。為今后高粱及其他糧食作物的育種改良提供了寶貴的遺傳資源，也為解決全球日益嚴峻的糧食問題奠定了重要的科研基礎(chǔ)。

論文鏈接： Emma S.Mace，et al..Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum.

Nature Communications，2013，4：2320.doi：10.1038／ncomms3320.

Abstract：Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500million of the world’s poorest people.Its small diploid genome and phenotypic diversity make it an ideal C4grass model as a complement to C3rice.Here we present high coverage（16-45×）resequenced genomes of 44sorghum lines representing the primary gene pool and spanning dimensions of geographic origin，end-use and taxonomic group.We also report the first resequenced genome of S.propinquum，identifying 8Mhigh-quality SNPs，1.9Mindels and specific gene loss and gain events in S.bicolor.We observe strong racial structure and a complex domestication history involving at least two distinct domestication events.These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum，providing an unmatched resource for the genetic improvement of sorghum and other grass species.

并非所有物種都因衰老而加速死亡

多數(shù)動物的死亡率會隨著年齡的增長而大幅增加。然而有些動物享有近乎恒定水平的繁殖力和死亡率。研究人員對比了46個物種的標準人口統(tǒng)計學(xué)模式，其中包括11種哺乳動物、12種其他脊椎動物、10種無脊椎動物、12種維管植物和一種綠藻，通過平均死亡率將生命周期中每一節(jié)點的死亡率區(qū)分開來，發(fā)現(xiàn)生命長度與衰老程度之間并沒有直接的聯(lián)系。有24個物種的死亡率隨著衰老而表現(xiàn)了最為突兀的增長，其中的11個物種具有相對較長的生命周期，而另13個物種則壽命相對較短。生命周期中的類似分裂也發(fā)生在那些死亡率并沒有明顯增加的物種中。這是第一次嘗試使跨物種的死亡率及存活比較標準化。

論文鏈接： Owen R.Jones，et al..Diversity of ageing across the tree of life.

Nature，2013，doi：10.1038／nature12789.

Abstract：Evolution drives，and is driven by，demography.A genotype moulds its phenotype’s age patterns of mortality and fertility in an environment；these two patterns in turn determine the genotype’s fitness in that environment.Hence，to understand the evolution of ageing，age patterns of mortality and reproduction need to be compared for species across the tree of life.However，few studies have done so and only for a limited range of taxa.Here we contrast standardized patterns over age for 11mammals，12other vertebrates，10invertebrates，12vascular plants and a green alga.Although it has been predicted that evolution should inevitably lead to increasing mortality and declining fertility with age after maturity，there is great variation among these species，including increasing，constant，decreasing，humped and bowed trajectories for both long-and short-lived species.This diversity challenges theoreticians to develop broader perspectives on the evolution of ageing and empiricists to study the demography of more species.

研究開發(fā)出抗旱水稻新品種

水稻種植需要大量水，所以干旱天氣是個大敵。日本研究人員對一種名為IR64的水稻（屬于秈稻）進行了基因研究，發(fā)現(xiàn)其DRO1基因有部分缺損。通過雜交，研究人員為IR64重新植入DRO1基因。結(jié)果發(fā)現(xiàn)其扎根深度達到以前的2倍以上。在水稻幾乎會絕收的嚴重干旱環(huán)境下，植入DRO1基因后，收獲量能夠達到通常水平的30%左右。這一抗旱水稻新品種有助于對抗干旱對水稻種植區(qū)的影響。此外，玉米等其他作物也有類似基因，所以此次的研究成果也有望促進開發(fā)出其他作物的耐旱新品種。

論文鏈接： Yusaku Uga，et al..Control of root system architecture by DEEPER ROOTING1increases rice yield under drought conditions.

Nature Genetics，2013，45：1097-1102.doi：10.1038／ng.2725.

Abstract：The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas1.Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING1（DRO1），a rice quantitative trait locus controlling root growth angle.DRO1is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity.Higher expression of DRO1increases the root growth angle，whereby roots grow in a more downward direction.Introducing DRO1into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting，which maintained high yield performance under drought conditions relative to the recipient cultivar.Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.

參與調(diào)控植物分枝（蘗）的生長發(fā)育基因發(fā)現(xiàn)

我國科學(xué)家首次在遺傳和生化層面證實D53蛋白可作為獨腳金內(nèi)酯信號途徑的抑制子，參與調(diào)控植物分枝（蘗）的生長發(fā)育。研究人員通過精細定位和圖位克隆，獲得了位于水稻第11號染色體短臂末端的DWARF53（D53）基因，結(jié)果表明，d53是一個獨腳金內(nèi)酯不敏感突變體。在獨腳金內(nèi)酯存在的條件下D53蛋白可與兩個已知的獨腳金內(nèi)酯信號分子D14、D3互作形成蛋白復(fù)合體，進而使得泛素化的D53蛋白特異地被蛋白酶體系統(tǒng)降解，從而誘導(dǎo)下游目標基因的表達以及獨腳金內(nèi)酯信號的響應(yīng)。該研究為植物，特別是農(nóng)作物的株型改良提供了重要的理論基礎(chǔ)。

論文鏈接： Feng Zhou，et al..D14-SCFD3-dependent degradation of D53regulates strigolactone signalling.

Nature，2013，504，406-410.doi：10.1038／nature12878.

Abstract：Strigolactones（SLs），a newly discovered class of carotenoid-derived phytohormones，are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi.Despite the rapid progress in elucidating the SL biosynthetic pathway，the perception and signalling mechanisms of SL remain poorly understood.Here we show that DWARF 53（D53）acts as a repressor of SL signalling and that SLs induce its degradation.We find that the rice（Oryza sativa）d53mutant，which produces an exaggerated number of tillers compared to wild-type plants，is caused by again-of-function mutation and is insensitive to exogenous SL treatment.The D53gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with theα／βhydrolase protein DWARF 14（D14）and the F-box protein DWARF 3（D3），two previously identified signalling components potentially responsible for SL perception.We demonstrate that，in a D14-and D3-dependent manner，SLs induce D53degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth.Our combined genetic and biochemical data reveal that D53acts as a repressor of the SL signalling pathway，whose hormone-induced degradation represents a key molecular link between SL perception and responses.

一種DNA修復(fù)酶可修復(fù)特定基因組不穩(wěn)定性

去乙?；?（SIRT1）是一種用來修復(fù)受損DNA的酶，由于去乙?；妇哂蟹乐勾竽X細胞凋亡的保護作用，研究發(fā)現(xiàn)，沒有SIRT1，神經(jīng)元無法修復(fù)由有毒化學(xué)物質(zhì)造成的DNA損傷，且SIRT1受到另一種酶的控制調(diào)節(jié)。該研究認為SIRT1可以修復(fù)患有神經(jīng)退行性疾病諸如阿爾茨海默氏癥和肌萎縮側(cè)索硬化癥（又名“漸凍人”癥，ALS）的小鼠體內(nèi)的基因組不穩(wěn)定性。

論文鏈接： Matthew M Dobbin，et al..SIRT1collaborates with ATM and HDAC1to maintain genomic stability in neurons.

Nature Neuroscience，2013，16，1008-1015.doi：10.1038／nn.3460.

Abstract：Defects in DNA repair have been linked to cognitive decline with age and neurodegenerative disease，yet the mechanisms that protect neurons from genotoxic stress remain largely obscure.We sought to characterize the roles of the NAD＋-dependent deacetylase SIRT1in the neuronal response to DNA double-strand breaks（DSBs）.We found that SIRT1was rapidly recruited to DSBs in postmitotic neurons，where it showed a synergistic relationship with ataxia telangiectasia mutated （ATM）.SIRT1 recruitment to breaks was ATM dependent；however，SIRT1also stimulated ATM autophosphorylation and activity and stabilized ATM at DSB sites.After DSB induction，SIRT1also bound the neuroprotective class I histone deacetylase HDAC1.We found that SIRT1deacetylated HDAC1and stimulated its enzymatic activity，which was necessary for DSB repair through the nonhomologous end-joining pathway.HDAC1mutations that mimic a constitutively acetylated state rendered neurons more susceptible to DNA damage，whereas pharmacological SIRT1activators that promoted HDAC1deacetylation also reduced DNA damage in two mouse models of neurodegeneration.We propose that SIRT1is an apical transducer of the DSB response and that SIRT1activation offers an important therapeutic avenue in neurodegeneration.

構(gòu)建小鼠基因組CRISPR導(dǎo)向RNAs文庫

CRISPR技術(shù)是指利用一段與靶序列相同的導(dǎo)向RNA來引導(dǎo)Cas9核酸酶對特異性靶向DNA進行識別和切割，造成DNA的雙鏈或單鏈斷裂，細胞隨后會對斷裂的DNA進行修復(fù)。利用該技術(shù)，研究人員構(gòu)建出了一個可誘導(dǎo)小鼠基因組全基因靶向突變的CRISPR導(dǎo)向RNA（gRNAs）綜合文庫。利用這些導(dǎo)向RNAs可以靶向和改變小鼠基因組中所有的基因，并已構(gòu)建小鼠突變胚胎干細胞，進而針對腐敗梭菌α毒素進行了一次遺傳篩查。研究小組靶向了26個已知與這種細菌毒素受體合成相關(guān)的基因，揭示出其中17個基因?qū)е铝丝剐园l(fā)生。同時，還發(fā)現(xiàn)了一些未知基因，這些基因發(fā)生突變賦予了對這種有毒物質(zhì)的抗性。

論文鏈接： Koike-Yusa H，et al..Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library.

Nature Biotechnology，doi：10.1038／nbt.2800.Published online：23December，2013.

Abstract：Identification of genes influencing aphenotype of interest is frequently achieved through genetic screening by RNA interference（RNAi）or knockouts.However，RNAi may only achieve partial depletion of gene activity，and knockout-based screens are difficult in diploid mammalian cells.Here we took advantage of the efficiency and high throughput of genome editing based on type II，clustered，regularly interspaced，short palindromic repeats（CRISPR）-CRISPR-associated （Cas）systems to introduce genome-wide targeted mutations in mouse embryonic stem cells（ESCs）.We designed 87，897guide RNAs（gRNAs）targeting 19，150mouse protein-coding genes and used a lentiviral vector to express these gRNAs in ESCs that constitutively express Cas9.Screening the resulting ESC mutant libraries for resistance to either Clostridium septicum alpha-toxin or 6-thioguanine identified 27 known and 4previously unknown genes implicated in these phenotypes.Our results demonstrate the potential for efficient loss-offunction screening using the CRISPR-Cas9system.