Discovery of novel intermediate forms redefines the fungal tree of life

Fungi are the principal degraders of biomass in terrestrial ecosystems and establish important interactions with plants and animals. However, our current understanding of fungal evolutionary diversity is incomplete and is based upon species amenable to growth in culture. These culturable fungi are typically yeast or filamentous forms, bound by a rigid cell wall rich in chitin. Evolution of this body plan was thought critical for the success of the Fungi, enabling them to adapt to heterogeneous habitats and live by osmotrophy: extracellular digestion followed by nutrient uptake. Here we investigate the ecology and cell biology of a previously undescribed and highly diverse form of eukaryotic life that branches with the Fungi, using environmental DNA analyses combined with fluorescent detection via DNA probes. This clade is present in numerous ecosystems including soil, freshwater and aquatic sediments. Phylogenetic analyses using multiple ribosomal RNA genes place this clade with Rozella, the putative primary branch of the fungal kingdom. Tyramide signal amplification coupled with group-specific fluorescence in situ hybridization reveals that the target cells are small eukaryotes of 3-5?μm in length, capable of forming a microtubule-based flagellum. Co-staining with cell wall markers demonstrates that representatives from the clade do not produce a chitin-rich cell wall during any of the life cycle stages observed and therefore do not conform to the standard fungal body plan. We name this highly diverse clade the cryptomycota in anticipation of formal classification.     

Species-specific responses of Late Quaternary megafauna to climate and humans

Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.     

Eocene global warming events driven by ventilation of oceanic dissolved organic carbon

'Hyperthermals' are intervals of rapid, pronounced global warming known from six episodes within the Palaeocene and Eocene epochs (～65-34 million years (Myr) ago). The most extreme hyperthermal was the ～170 thousand year (kyr) interval of 5-7 °C global warming during the Palaeocene-Eocene Thermal Maximum (PETM, 56?Myr ago). The PETM is widely attributed to massive release of greenhouse gases from buried sedimentary carbon reservoirs, and other, comparatively modest, hyperthermals have also been linked to the release of sedimentary carbon. Here we show, using new 2.4-Myr-long Eocene deep ocean records, that the comparatively modest hyperthermals are much more numerous than previously documented, paced by the eccentricity of Earth's orbit and have shorter durations (～40?kyr) and more rapid recovery phases than the PETM. These findings point to the operation of fundamentally different forcing and feedback mechanisms than for the PETM, involving redistribution of carbon among Earth's readily exchangeable surface reservoirs rather than carbon exhumation from, and subsequent burial back into, the sedimentary reservoir. Specifically, we interpret our records to indicate repeated, large-scale releases of dissolved organic carbon (at least 1,600 gigatonnes) from the ocean by ventilation (strengthened oxidation) of the ocean interior. The rapid recovery of the carbon cycle following each Eocene hyperthermal strongly suggests that carbon was re-sequestered by the ocean, rather than the much slower process of silicate rock weathering proposed for the PETM. Our findings suggest that these pronounced climate warming events were driven not by repeated releases of carbon from buried sedimentary sources, but, rather, by patterns of surficial carbon redistribution familiar from younger intervals of Earth history.     

基于参考说话人模型和双层结构的说话人辨认

为了提高基于Gauss混合模型通用背景模型(GMM-UBM)的说话人辨认系统的运算效率,提出一种基于参考说话人模型的双层结构用于目标说话人剪枝,采用矢量量化方法从目标说话人模型集合中训练参考说话人模型,利用语音与参考说人模型的偏差来描述说话人的发音特性,将辨认语音偏差向量和目标说话人偏差向量的相似性作为距离度量来进行目标说话人剪枝。实验结果表明:在基于GMM-UBM的说话人辨认系统中,对包含5 200个目标说话人和1 000个集外说话人的测试集进行开集辨认的条件下,在提高辨认的运算效率12.5倍的同时识别率仅下降0.3%。     

Association of dwarfism and floral induction with a grape 'green revolution' mutation

The transition from vegetative to reproductive growth is an essential process in the life cycle of plants. Plant floral induction pathways respond to both environmental and endogenous cues and much has been learnt about these genetic pathways by studying mutants of Arabidopsis. Gibberellins (GAs) are plant growth regulators important in many aspects of plant growth and in Arabidopsis they promote flowering. Here we provide genetic evidence that GAs inhibit flowering in grapevine. A grapevine dwarf mutant derived from the L1 cell layer of the champagne cultivar Pinot Meunier produces inflorescences along the length of the shoot where tendrils are normally formed. The mutated gene associated with the phenotype is a homologue of the wheat 'green revolution' gene Reduced height-1 (ref. 6) and the Arabidopsis gene GA insensitive (GAI). The conversion of tendrils to inflorescences in the mutant demonstrates that the grapevine tendril is a modified inflorescence inhibited from completing floral development by GAs.     

Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry

The bacteria causing diphtheria, whooping cough, cholera and other diseases secrete mono-ADP-ribosylating toxins that modify intracellular proteins. Here, we describe four structures of a catalytically active complex between a fragment of Pseudomonas aeruginosa exotoxin A (ETA) and its protein substrate, translation elongation factor 2 (eEF2). The target residue in eEF2, diphthamide (a modified histidine), spans across a cleft and faces the two phosphates and a ribose of the non-hydrolysable NAD+ analogue, betaTAD. This suggests that the diphthamide is involved in triggering NAD+ cleavage and interacting with the proposed oxacarbenium intermediate during the nucleophilic substitution reaction, explaining the requirement of diphthamide for ADP ribosylation. Diphtheria toxin may recognize eEF2 in a manner similar to ETA. Notably, the toxin-bound betaTAD phosphates mimic the phosphate backbone of two nucleotides in a conformational switch of 18S rRNA, thereby achieving universal recognition of eEF2 by ETA.     

What’s right about Carnap, Neurath and the Left Vienna Circle thesis: a refutation

This paper rejects as unfounded a recent criticism of research on the so-called left wing of the Vienna Circle and the claim that it sported a political philosophy of science. The demand for ‘specific, local periodized claims’ is turned against the critic. It is shown (i) that certain criticisms of Red Vienna’s leading party cannot be transferred to the members of the Circle involved in popular education, nor can criticism of Carnap’s Aufbau be transferred to Neurath’s unified science project; (ii) that neither with regard to Carnap nor to Neurath does the criticism raise points that either engage with the thesis proposed or stand up to closer scrutiny; (iii) that the main thesis attacked is just what I had warned the claim that the Vienna Circle had a political philosophy of science should not be understood as. The question whether theirs is ‘political enough’ today can and should be discussed without distortion of the historical record.     

Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index

Obesity is globally prevalent and highly heritable, but its underlying genetic factors remain largely elusive. To identify genetic loci for obesity susceptibility, we examined associations between body mass index and ～ 2.8 million SNPs in up to 123,865 individuals with targeted follow up of 42 SNPs in up to 125,931 additional individuals. We confirmed 14 known obesity susceptibility loci and identified 18 new loci associated with body mass index (P < 5 × 10??), one of which includes a copy number variant near GPRC5B. Some loci (at MC4R, POMC, SH2B1 and BDNF) map near key hypothalamic regulators of energy balance, and one of these loci is near GIPR, an incretin receptor. Furthermore, genes in other newly associated loci may provide new insights into human body weight regulation.