Global landscape of HIV-human protein complexes

Human immunodeficiency virus (HIV) has a small genome and therefore relies heavily on the host cellular machinery to replicate. Identifying which host proteins and complexes come into physical contact with the viral proteins is crucial for a comprehensive understanding of how HIV rewires the host's cellular machinery during the course of infection. Here we report the use of affinity tagging and purification mass spectrometry to determine systematically the physical interactions of all 18 HIV-1 proteins and polyproteins with host proteins in two different human cell lines (HEK293 and Jurkat). Using a quantitative scoring system that we call MiST, we identified with high confidence 497 HIV-human protein-protein interactions involving 435 individual human proteins, with ～40% of the interactions being identified in both cell types. We found that the host proteins hijacked by HIV, especially those found interacting in both cell types, are highly conserved across primates. We uncovered a number of host complexes targeted by viral proteins, including the finding that HIV protease cleaves eIF3d, a subunit of eukaryotic translation initiation factor 3. This host protein is one of eleven identified in this analysis that act to inhibit HIV replication. This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection.     

Enterotypes of the human gut microbiome

Our knowledge of species and functional composition of the human gut microbiome is rapidly increasing, but it is still based on very few cohorts and little is known about variation across the world. By combining 22 newly sequenced faecal metagenomes of individuals from four countries with previously published data sets, here we identify three robust clusters (referred to as enterotypes hereafter) that are not nation or continent specific. We also confirmed the enterotypes in two published, larger cohorts, indicating that intestinal microbiota variation is generally stratified, not continuous. This indicates further the existence of a limited number of well-balanced host-microbial symbiotic states that might respond differently to diet and drug intake. The enterotypes are mostly driven by species composition, but abundant molecular functions are not necessarily provided by abundant species, highlighting the importance of a functional analysis to understand microbial communities. Although individual host properties such as body mass index, age, or gender cannot explain the observed enterotypes, data-driven marker genes or functional modules can be identified for each of these host properties. For example, twelve genes significantly correlate with age and three functional modules with the body mass index, hinting at a diagnostic potential of microbial markers.     

年青恒星体喷流理论和观测

年青恒星体中喷流现象很普遍。大量天体物理文献瞄准了活动星系核、共生恒星、行星状星云和X射线双星中的物质喷发现象。在恒星形成中基本开放的问题之一是物理机制。物质从原恒星系统喷发，进入喷流。部分喷流控制系统角动力，并且在最初的几百万年里演化。在大尺度上，喷流为恒星形成和演化注入动力。     

Polysialic acids: potential in improving the stability and pharmacokinetics of proteins and other therapeutics

Naturally occurring polymers of N-acetylneuraminic acid (polysialic acids) are biodegradable, highly hydrophilic and have no known receptors in the body. Following intravenous injection, polysialic acids exhibit long half-lives in the blood circulation and have therefore been proposed as carriers of short-lived drugs and small peptides. In addition, shorter-chain polysialic acids can be used as a means to increase the circulatory half-life of proteins and thus serve as an alternative to the nonbiodegradable monomethoxypoly(ethylene glycol). Recent work has shown that covalent coupling of a low molecular weight polysialic acid (colominic acid) to catalase and asparaginase leads to a considerable increase of enzyme stability in the presence of proteolytic enzymes or blood plasma. Comparative studies in vivo with polysialylated and intact asparaginase revealed that polysialylation significantly increases the half-life of the enzyme. The highly hydrophilic and innocuous nature of polysialic acids renders them suitable as a means to prolong the circulation of peptides and proteins.     

The genome of Theobroma cacao

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.     

A study of triphorid larvae and post-larvae at the Campos Basin deep-sea floor,southeastern Brazil (Gastropoda: Triphoroidea)

Triphoridae is a family of marine microgastropods, with hundreds of species described especially from shallow waters, comprising planktotrophic and non-planktotrophic development modes. The present study focusses on an interesting finding of the deep-sea Oceanprof Expedition, conducted in Campos Basin (southeastern Brazil), in which triphorid larvae and a few post-larvae were profusely sampled at the slope, leading us to three main questions: (1) What species of Triphoridae do these larvae belong to? (2) Why were so many triphorid larvae found at the site? and (3) What does the presence of post-larvae mean? We show that all the larvae belong to genera or species present in the Campos Basin continental shelf. Some speculations are made about the great abundance of larvae in the slope, especially to vertical migrations of larvae, and about mesh size, in addition to possible differences of larval ecology between triphorids and the closely related Cerithiopsidae. Two possible explanations are indicated for the presence of post-larvae: mass effect (formation of pseudopopulations) or mid-water metamorphosis (spontaneous metamorphosis at the water column), with the latter being the more likely scenario. Despite being essentially theoretical, the present study aims to develop new insights into the larval ecology of these small gastropods, and to furnish a base for future tests.     

Synopsis of the deep-sea groups of Triphoroidea (Gastropoda)

The marine gastropod superfamily Triphoroidea is composed of three families: Triphoridae and Cerithiopsidae are usually associated with shallow waters, and Newtoniellidae is historically associated with the deep sea. We provide an extensive review of the literature and delineate the groups within the three families that are truly linked to the deep sea, with reference to their developmental mode. Two genera of Triphoridae, Strobiligera and Inella, are commonly found in deep waters, and Metaxia presents some species with apparently wide depth ranges. Some deep-sea genera currently placed in Cerithiopsidae, such as Ektonos and Krachia, are very similar to Newtoniellidae; a phylogeny of the superfamily is needed to clarify the distinction of the two families. The majority of Triphoroidea species from the deep sea undergo non-planktotrophic development, although planktotrophy is not uncommon.