Circles

Molecular and Cellular Biochemistry -     

Flower scents from the Pacific

For a long time, exotic scents from the islands of the South Pacific have universally been appreciated. Most frequently, fragrant flowers (e.g., frangipani, jasmine sambac, tiaré, pua kenikeni) are used locally for ornamental purposes such as flower garlands (leis). Despite their powerful and delightful fragrance, very few of these flowers have been commercially employed in this part of the world for perfume manufacturing. Creative perfumers are nevertheless strongly interested to better understand these fragrances and to use them, either genuine or artificially reconstituted. Analytical results on the fragrance of these flowers are reported, together with some economical considerations.     

CpG特征结构与树突状细胞

近年来的研究表明 :ＣｐＧ特征结构是脊椎动物免疫系统识别微生物ＤＮＡ并产生针对抗原的保护性免疫反应的主要机制 ,它在体内及体外均能诱导以Ｔｈ1细胞为主的高水平、高特异性的细胞免疫应答 ;是质粒ＤＮＡ疫苗及裸ＤＮＡ疫苗诱导机体免疫应答的原因之一 ,在临床实验中ＣｐＧ ＯＤＮ已被用作抗原疫苗、ＤＮＡ疫苗治疗肿瘤、变态反应性疾病的强有力佐剂。ＣｐＧ特征结构能够诱导机体产生以Ｔｈ1细胞为主的细胞免疫应答是因为它能够作用于Ｔ细胞、Ｂ细胞、ＮＫ细胞、巨噬细胞及树突状细胞等免疫细胞。树突状细胞是机体最主要的专职抗原呈递…     

Motifs in brain networks

Complex brains have evolved a highly efficient network architecture whose structural connectivity is capable of generating a large repertoire of functional states. We detect characteristic network building blocks (structural and functional motifs) in neuroanatomical data sets and identify a small set of structural motifs that occur in significantly increased numbers. Our analysis suggests the hypothesis that brain networks maximize both the number and the diversity of functional motifs, while the repertoire of structural motifs remains small. Using functional motif number as a cost function in an optimization algorithm, we obtain network topologies that resemble real brain networks across a broad spectrum of structural measures, including small-world attributes. These results are consistent with the hypothesis that highly evolved neural architectures are organized to maximize functional repertoires and to support highly efficient integration of information.     

富脯氨酸模体研究进展

综述了近年来富脯氨酸模体的研究进展状况,并将其分为PxxP核心序列模体、聚脯氨酸模体、PPxY核心序列模体以及其他类型的模体4类,论述了富脯氨酸膜体的生物学功能及其常出现的原因.     

用网络方法识别生物序列motif

生物序列motif的识别是后基因组时代的一个核心问题。本文首先回顾了识别motif的几种主要算法,然后根据motif的重要性和随机性介绍了利用网络识别motif的两种具有代表性的方法：一种是建立一个随机网络混合模型,利用EM算法识别其中随机的网络motif;另一种用修正的参数流算法过滤出其中的最大密度予图,即为生物序列motif,并指出这两种方法的优劣,最后还对今后研究方向给出了讨论。     

REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply the method to human data and discover a number of potentially new repeats sequences that have been missed by previous repeat annotations. Many of these sequences are incorporated into various parasite genomes, possibly because the filtering process for host DNA involved in the sequencing of the parasite genomes failed to exclude the host derived repeat sequences. REPdenovo is a new powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families. The software tool, REPdenovo, is available for download at https://github.com/Reedwarbler/REPdenovo.     

Pollinator-Mediated Selection on Flower Color,Flower Scent and Flower Morphology of Hemerocallis: Evidence from Genotyping Individual Pollen Grains On the Stigma

To trace the fate of individual pollen grains through pollination processes, we determined genotypes of single pollen grains deposited on Hemerocallis stigmas in an experimental mixed-species array. Hemerocallis fulva, pollinated by butterflies, has diurnal, reddish and unscented flowers, and H. citrina, pollinated by hawkmoths, has nocturnal, yellowish and sweet scent flowers. We observed pollinator visits to an experimental array of 24 H. fulva and 12 F2 hybrids between the two species (H. fulva and H. citrina) and collected stigmas after every trip bout of swallowtail butterflies or hawkmoths. We then measured selection by swallowtail butterflies or hawkmoths through male and female components of pollination success as determined by single pollen genotyping. As expected, swallowtail butterflies imposed selection on reddish color and weak scent: the number of outcross pollen grains acquired is a quadratic function of flower color with the maximum at reddish color, and the combined pollination success was maximal at weak scent (almost unrecognizable for human). This explains why H. fulva, with reddish flowers and no recognizable scent, is mainly pollinated by swallowtail butterflies. However, we found no evidence of hawkmoths-mediated selection on flower color or scent. Our findings do not support a hypothesis that yellow flower color and strong scent intensity, the distinctive floral characteristics of H. citrina, having evolved in adaptations to hawkmoths. We suggest that the key trait that triggers the evolution of nocturnal flowers is flowering time rather than flower color and scent.     

CpG模体的免疫激活机制及应用

CpG模体是一些在机体内外具有强烈免疫激活功能的寡聚脱氧核苷酸短序列。章综述了近年来有关CpG模体作用机制及其应用方面的研究进展。在机制方面,着重对CpGDNA细胞激活和信号转导两方面进行了详尽的阐述;在应用方面,重点介绍了其作为疫苗佐剂和免疫性疾病治疗药物的研究现状。     

Flower: extracting information from pyrosequencing data

The SFF file format produced by Roche's 454 sequencing technology is a compact, binary format that contains the flow values that are used for base and quality calling of the reads. Applications, e.g. in metagenomics, often depend on accurate sequence information, and access to flow values is important to estimate the probability of errors. Unfortunately, the programs supplied by Roche for accessing this information are not publicly available. Flower is a program that can extract the information contained in SFF files, and convert it to various textual output formats. AVAILABILITY: Flower is freely available under the General Public License.     

Motifs involved in protein-protein interactions

Summary Interactions between proteins are extremely variable. However, in the dimeric proteins comprised of regular motifs, interface interactions are similar to those that stabilize monomers. Additional stability is gained by converting loops within motifs or domains to linkers across interfaces. In multi-domain proteins, interactions can be greatly effected by the conformation of linkers between domains. Complex association of subunits, involving higher rotational symmetry or cubic symmetry, frequently involves motif sharing across interfaces.