SeSaMe:Metagenome Sequence Classification of Arbuscular Mycorrhizal Fungi-associated Microorganisms

Arbuscular mycorrhizal fungi (AMF) are plant root symbionts that play key roles in plant growth and soil fertility. They are obligate biotrophic fungi that form coenocytic multinucleated hyphae and spores. Numerous studies have shown that diverse microorganisms live on the surface of and inside their mycelia, resulting in a metagenome when whole-genome sequencing (WGS) data are obtained from sequencing AMF cultivated in vivo. The metagenome contains not only the AMF sequences, but also those from associated microorganisms. In this study, we introduce a novel bioinformatics program, Spore-associated Symbiotic Microbes (SeSaMe), designed for taxonomic classification of short sequences obtained by next-generation DNA sequencing. A genus-specific usage bias database was created based on amino acid usage and codon usage of a three consecutive codon DNA 9-mer encoding an amino acid trimer in a protein secondary structure. The program distinguishes between coding sequence (CDS) and non-CDS, and classifies a query sequence into a genus group out of 54 genera used as reference. The mean percentages of correct predictions of the CDS and the non-CDS test sets at the genus level were 71% and 50% for bacteria, 68% and 73% for fungi (excluding AMF), and 49% and 72% for AMF (Rhizophagus irregularis), respectively. SeSaMe provides not only a means for estimating taxonomic diversity and abundance but also the gene reservoir of the reference taxonomic groups associated with AMF. Therefore, it enables users to study the symbiotic roles of associated microorganisms. It can also be applicable to other microorganisms as well as soil metagenomes. SeSaMe is freely available at www.fungalsesame.org.     

Molecular pathogenesis of sporadic prion diseases in man

The yeast, fungal and mammalian prions determine heritable and infectious traits that are encoded in alternative conformations of proteins. They cause lethal sporadic, familial and infectious neurodegenerative conditions in man, including Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker syndrome (GSS), kuru, sporadic fatal insomnia (SFI) and likely variable protease-sensitive prionopathy (VPSPr). The most prevalent of human prion diseases is sporadic (s)CJD. Recent advances in amplification and detection of prions led to considerable optimism that early and possibly preclinical diagnosis and therapy might become a reality. Although several drugs have already been tested in small numbers of sCJD patients, there is no clear evidence of any agent’s efficacy. Therefore, it remains crucial to determine the full spectrum of sCJD prion strains and the conformational features in the pathogenic human prion protein governing replication of sCJD prions. Research in this direction is essential for the rational development of diagnostic as well as therapeutic strategies. Moreover, there is growing recognition that fundamental processes involved in human prion propagation – intercellular induction of protein misfolding and seeded aggregation of misfolded host proteins – are of far wider significance. This insight leads to new avenues of research in the ever-widening spectrum of age-related human neurodegenerative diseases that are caused by protein misfolding and that pose a major challenge for healthcare.     

The Constitutional Amine of Antibiotic YA-56

In addition to the previously reported six amino acids and two carbohydrates (one disaccharide), 3-aminopropionamidine was isolated as a constituent from the acid hydrolyzate of the antibiotic YA–56X, one of the major component of antibiotic YA–56 complex. Based on the hitherto found informations, structural comparison of the antibiotic YA–56 X and Y was made with phleomycins, bleomycins, zorbamycin and zorbonomycin B to which antibiotic YA–56 closely related. Among those, zorbamycin was identical with antibiotic YA–56 X.     

Effect of Ageing on the Oxidative Browning of Sugar-Amino Acid Model Systems

Sugar-amino acid model systems were aged for 3 months under anaerobic or aerobic conditions. Subsequently, these aged model systems were stored for 2 weeks at 37°C under aerobic conditions to examine “oxidative browning.” The results obtained were as follows:

1. The oxidative browning of the model systems increased with increase of the ageing period. Fe²⁺ increased the effects of the ageing.

2. The model systems aged under anaerobic conditions darkened more than those aged under aerobic conditions during storage for 2 weeks.

3. An Amadori rearrangement product, 1-deoxy-1-glycino-d-fructcse was isolated from the aged glucose-glycine model system and it caused a marked increase in the rate of the oxidative browning. Therefore, Amadori rearrangement products are considered to be important precursors in the oxidative browning reaction.

     

Quantifying spatial and temporal variation of North Pacific fin whale (Balaenoptera physalus) acoustic behavior

In order to help develop hypotheses of connectivity among North Pacific fin whales, we examine recordings from 10 regions collected in the spring and fall. We develop a Random Forest model to classify fin whale note types that avoids manual note classification errors. We also present a method that objectively quantifies the note and pattern composition of recordings. We find that fin whale recordings near Hawaii have distinctive patterns, similar to those found in other regions in the central North Pacific, suggesting potential migration pathways. Our results are consistent with previous studies that suggest there may be two different populations utilizing the Chukchi Sea and central Aleutians in the fall and mix to some degree in the southern Bering Sea. Conversely, we found little difference between spring and fall recordings in the eastern Gulf of Alaska, suggesting some residency of whales in this region. This is likely due to fine scale similarities of calls among the inshore regions of British Columbia, while offshore areas are being utilized by whales traveling from various distant areas. This study shows how our novel approach to characterize recordings is an objective and informative way to standardize spatial and temporal comparisons of fin whale recordings.     

蕨类植物的鳞片特征及演化I: 凤尾蕨科

鳞片是蕨类植物体表常见附属物, 是蕨类植物非常显著的分类学特征。凤尾蕨科(Pteridaceae)在蕨类植物系统发育中的位置关系多次发生了变化, 不同学者对该科中包含的类群也有着不同的观点。通过对该科76种植物的鳞片进行取材, 利用解剖镜观察拍照, 对各属鳞片特征进行描述。结果显示, 鳞片特征在不同的属和亚科之间具有明显的形态差异。用GenBank数据库中的rbcL基因序列对所研究物种进行系统发育重建, 并对鳞片的边缘特征和筛孔类型进行祖先性状重建, 结果表明, 全缘型鳞片和均质型鳞片是凤尾蕨科鳞片的祖征性状, 非全缘类型和透明筛孔类型的鳞片是在后期演化过程中形成的特征。此外, 透明和不透明类型的筛孔其形成可能与蕨类植物生活环境中的光照强度有关。     

Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming

With more than 300 species, the Magnoliaceae family represents a major Magnoliid lineage that is disjunctly distributed in Asia and the New World. The classification of Magnolia s.l. has been highly controversial among taxonomists, varying from one genus with several subgenera, sections, and subsections to several (up to 16) genera. We conducted a comprehensive phylogenetic study of Magnoliaceae on the basis of sequences of the complete chloroplast genomes with a broad taxon sampling of 86 species. The phylogenetic analyses strongly support 15 major clades within Magnolia s.l. due to the non‐monophyly of subgen. Magnolia, the previous subgeneric treatment that recognizes three subgenera, is not supported. Based on the phylogenetic, morphological, and geographic evidence, we recognize two subfamilies in Magnoliaceae: Liriodendroideae and Magnolioideae, each with one genus, Liriodendron and Magnolia, respectively. Magnolia is herein classified into 15 sections: sects. Magnolia, Manglietia, Michelia, Gwillimia, Gynopodium, Kmeria, Maingola, Oyama, Rytidospermum, Splendentes, Talauma, Tuliparia, Macrophylla, Tulipastrum, and Yulania.     

安徽沿淮湖泊湿地水鸟资源调查

2008年6月至2009年5月,采用路线调查法和定点观察法对安徽沿淮的东西湖、瓦埠湖、龙子湖、沱湖和女山湖5个湖泊湿地的水鸟资源进行了调查,共记录湿地水鸟61种,隶属于7目13科.按居留型可分为冬候鸟32种(占52.46%),夏候鸟14种(占22.95%),留鸟2种(占3.28%),旅鸟13种(占21.31%);按生态...