Multi‐gene phylogenetic analysis reveals that shochu‐fermenting Saccharomyces cerevisiae strains form a distinct sub‐clade of the Japanese sake cluster

Shochu is a traditional Japanese distilled spirit. The formation of the distinguishing flavour of shochu produced in individual distilleries is attributed to putative indigenous yeast strains. In this study, we performed the first (to our knowledge) phylogenetic classification of shochu strains based on nucleotide gene sequences. We performed phylogenetic classification of 21 putative indigenous shochu yeast strains isolated from 11 distilleries. All of these strains were shown or confirmed to be Saccharomyces cerevisiae, sharing species identification with 34 known S. cerevisiae strains (including commonly used shochu, sake, ale, whisky, bakery, bioethanol and laboratory yeast strains and clinical isolate) that were tested in parallel. Our analysis used five genes that reflect genome‐level phylogeny for the strain‐level classification. In a first step, we demonstrated that partial regions of the ZAP1, THI7, PXL1, YRR1 and GLG1 genes were sufficient to reproduce previous sub‐species classifications. In a second step, these five analysed regions from each of 25 strains (four commonly used shochu strains and the 21 putative indigenous shochu strains) were concatenated and used to generate a phylogenetic tree. Further analysis revealed that the putative indigenous shochu yeast strains form a monophyletic group that includes both the shochu yeasts and a subset of the sake group strains; this cluster is a sister group to other sake yeast strains, together comprising a sake‐shochu group. Differences among shochu strains were small, suggesting that it may be possible to correlate subtle phenotypic differences among shochu flavours with specific differences in genome sequences. Copyright © 2017 John Wiley & Sons, Ltd.     

A study of chlorophyll-like and phycobilin pigments in the C endosymbiont of the apple- snail <i>Pomacea canaliculata</i>

Pigments present in the brown-greenish C morph of an intracellular endosymbiont of Pomacea canaliculata were investigated. Acetone extracts of the endosymbiotic corpuscles showed an absorption spectrum similar to that of chlorophylls. Three fractions obtained from silica gel column chromatography of the acetone extracts (C_I , C_II and C_III ), were studied by positive ion fast atom bombardment-mass spectrometry (FAB–MS) and hydrogen-nuclear magnetic resonance (H-NMR). Results indicated the presence of (1) a sterol in the yellow colored C_I fraction; (2) a mixture of pheophorbides a and b in the major green fraction, C_II; and (3) a modified pheophorbide a in the smaller green fraction, C_III . Aqueous extracts of the C endosymbiont did not show evidence of the occurrence of C-phycocyanin, allophycocyanin or phycoerithrin (light absorption, fluorescence emission, and electrophoresis of the protein moieties) while cyanobacterial cells (Nostoc sp.) showed evidence of C-phycocyanin and allophycocyanin. The possible phylogenetic and functional significance of the pigments present in the C endosymbiont is discussed.     

Bacillus amyloliquefaciens KHQH-1的鉴定及其抗菌活性初步研究

为了探寻新的具有防腐保鲜功能的微生物资源,前期从柑橘防腐保鲜研究过程中,分离纯化得到1株具有抗菌活性的细菌。该研究对该菌进行了形态、生化和分子生物学等鉴定,确定该菌株属于芽孢杆菌属,命名为Bacillus amyloliquefaciens KHQH-1。通过NCBI平台BLAST进行序列比对,结合Clustalw和Mega 7.0等软件进行序列分析和构建系统发育树,确立了该菌株在系统发育上的地位。采用点植法和滤纸片法研究了KHQH-1对几种食品中常见霉菌和细菌的拮抗效果,结果表明,KHQH-1对根霉(Rhizopus spp.)、米曲霉(Aspergillus oryzae)有一定抑制效果,对食品中常见霉菌黄曲霉(Aspergillus flavus)、青霉(Penicillium spp.)、绿色木霉(Trichoderma viride)具有较强抑制效果,其抑菌圈大小分别为13.70、9.30和10.87 mm;KHQH-1对食品中常见细菌金黄色葡萄球菌(Staphylococcus aureus)和大肠杆菌(Escherichia coli)均有一定抑制作用,其抑菌圈分别为3.20和8.20 mm。这为更进一步探索天然产物防腐保鲜技术和微生物制剂的开发与应用提供了一定的理论与技术参考。     

Phylogenetic relationships among species of Saccharomyces, Schizosaccharomyces, Debaryomyces and Schwanniomyces determined from partial ribosomal RNA sequences

Species of the genera Saccharomyces, Schizosaccharomyces, Debaryomyces and Schwanniomyces were compared from their extent of divergence in three regions from small (18S) and large (25S) subunit ribosomal RNAs comprising a total of 900 nucleotides. With the exception of the closely related Saccharomyces bayanus and S. pastorianus, which appear to have identical sequences, all other species could be distinguished by nucleotide differences in a variable region of the large subunit, and genus-specific nucleotides were discernible in all three regions. The taxon D. tamarii differed markedly from other species and is excluded from Debaryomyces. By contrast, Schwanniomyces occidentalis showed few nucleotide differences with Debaryomyces spp. and its transfer to Debaryomyces is proposed. Schizosaccharomyces proved to be somewhat more divergent than Saccharomyces and Debaryomyces, but species differences appear insufficient for dividing the genus. Some of the factors influencing estimates of phylogenetic distances from rRNA sequences are discussed.     

从发生学角度考察当代芬兰设计

文章从芬兰设计发展的各个要素入手,先后从地理环境,历史背景,政治经济,国民素质与政府支持等外部客观原因,及设计师、设计公司、设计教育等主观因素进行剖析,解读芬兰何以成为世界优秀设计的发源地。尝试从发生学的角度,以逻辑的方式推演和梳理芬兰设计发展中的各种推动因素。     

海带配子体叶绿素a/c结合蛋白基因lhcf6的序列特征与系统发生分析

通过根据糖海带(Laminaria saccharina)叶绿素 a/c 结合蛋白基因 lhcf6 的 cDNA 序列设计的引物和 PCR 方法获得了海带(L.japonica)配子体 llwf6 基因的 cDNA 全长序列(GenBank 登录号:DQ250739).该序列的开放阅读框(ORF)与糖海带 lhcf6 编码序列的相似性高达 99%,而两非翻译区(UTR)序列的相似性只有94%.经推测,海带配子体 lhcf6基因序列的 ORF 编码一个含 218 个氨基酸的前体蛋白 LHCF6,其氨基端的 40 个氨基酸组成跨质体内质网和叶绿体膜的信号肽,跨膜酶切后变为含 178 个氨基酸的成熟蛋白,它的分子量为 19.3 kD,等电点为 4.88.预测的成熟蛋白 IJ-ICF6 高级结构存在 2 个保守性的β折叠和 3 个跨类囊体膜的 a 螺旋区.根据海带配子体 LHCF6 成熟蛋白以及 GenBank 中 12 个同源蛋白质的氨基酸序列所构建的 Neighbor-joining 分子进化树,显示藻类在光捕获蛋白氨基酸序列水平上存在着蓝藻与红藻、杂色藻类、裸藻与绿藻等三个方向的演化途径,其中裸藻和绿藻与高等植物的亲缘关系更近.     

Connexins during 500 Million Years—From Cyclostomes to Mammals

It was previously shown that the connexin gene family had relatively similar subfamily structures in several vertebrate groups. Still, many details were left unclear. There are essentially no data between tunicates, which have connexins that cannot be divided into the classic subfamilies, and teleosts, where the subfamilies are easily recognized. There are also relatively few data for the groups that diverged between the teleosts and mammals. As many of the previously analyzed genomes have been improved, and many more genomes are available, we reanalyzed the connexin gene family and included species from all major vertebrate groups. The major results can be summarized as follows: (i) The same connexin subfamily structures are found in all Gnathostomata (jawed vertebrates), with some variations due to genome duplications, gene duplications and gene losses. (ii) In contrast to previous findings, birds do not have a lower number of connexins than other tetrapods. (iii) The cyclostomes (lampreys and hagfishes) possess genes in the alpha, beta, gamma and delta subfamilies, but only some of the genes show a phylogenetic affinity to specific genes in jawed vertebrates. Thus, two major evolutionary transformations have occurred in this gene family, from tunicates to cyclostomes and from cyclostomes to jawed vertebrates.     

Avoidance and Potential Remedy Solutions of Chimeras in Reconstructing the Phylogeny of Aphids Using the 16S rRNA Gene of Buchnera: A Case in Lachninae (Hemiptera)

It is known that PCR amplification of highly homologous genes from complex DNA mixtures can generate a significant proportion of chimeric sequences. The 16S rRNA gene is not only widely used in estimating the species diversity of endosymbionts in aphids but also used to explore the co-diversification of aphids and their endosymbionts. Thus, chimeric sequences may lead to the discovery of non-existent endosymbiont species and mislead Buchnera-based phylogenetic analysis that lead to false conclusions. In this study, a high probability (6.49%) of chimeric sequence occurrence was found in the amplified 16S rRNA gene sequences of endosymbionts from aphid species in the subfamily Lachninae. These chimeras are hybrid products of multiple parent sequences from the dominant species of endosymbionts in each corresponding host. It is difficult to identify the chimeric sequences of a new or unidentified species due to the high variability of their main parent, Buchnera aphidicola, and because the chimeric sequences can confuse the phylogenetic analysis of 16S rRNA gene sequences. These chimeras present a challenge to Buchnera-based phylogenetic research in aphids. Thus, our study strongly suggests that using appropriate methods to detect chimeric 16S rRNA sequences may avoid some false conclusions in endosymbiont-based aphid research.     

Comparison of Silks from Pseudoips prasinana and Bombyx mori Shows Molecular Convergence in Fibroin Heavy Chains but Large Differences in Other Silk Components

Many lepidopteran larvae produce silk feeding shelters and cocoons to protect themselves and the developing pupa. As caterpillars evolved, the quality of the silk, shape of the cocoon, and techniques in forming and leaving the cocoon underwent a number of changes. The silk of Pseudoips prasinana has previously been studied using X-ray analysis and classified in the same category as that of Bombyx mori, suggesting that silks of both species have similar properties despite their considerable phylogenetic distance. In the present study, we examined P. prasinana silk using ‘omics’ technology, including silk gland RNA sequencing (RNA-seq) and a mass spectrometry-based proteomic analysis of cocoon proteins. We found that although the central repetitive amino acid sequences encoding crystalline domains of fibroin heavy chain molecules are almost identical in both species, the resulting fibers exhibit quite different mechanical properties. Our results suggest that these differences are most probably due to the higher content of fibrohexamerin and fibrohexamerin-like molecules in P. prasinana silk. Furthermore, we show that whilst P. prasinana cocoons are predominantly made of silk similar to that of other Lepidoptera, they also contain a second, minor silk type, which is present only at the escape valve.