RNA SEQUENCE DATA IN PHYLOGENETIC RECONSTRUCTION: TESTING THE LIMITS OF ITS RESOLUTION

Abstract— 18S ribosomal RNA sequences from 11 echinoderms are analysed using parsimony to investigate phylogenetic relationships. Their estimated divergence limes range from less than 20 Ma to more than 550 Ma before present. Phylogenies based on 18S rRNA sequence data are compared with well-established morphological phylogenies to discover at what evolutionary distance the two approaches start to produce incongruent results. Three regions of the 18S rRNA molecule are analysed separately and together, and paired and unpaired sites are also treated separately and combined.
Results show that a parsimony analysis of sequence data produces reliable results only when taxa have diverged more recently than about 100 Ma. At greater evolutionary distances (up to 250 Ma), paired nucleotides produce more reliable results than unpaired, while paired and unpaired data combined produce intermediate results. All trees within about 1% of the most parsimonious solution ought to be accepted. Transversions give results almost as reliable as paired regions though there were relatively few informative sites. The relationships of echinoderm classes, which diverged 450–550 Ma ago, are unresolved by 18S rRNA data.     

马槟榔甜味蛋白N-和C-末端部分氨基酸顺序的测定

从马槟榔(Capparis masaikai)种子中曾分离出二种甜味蛋白,称为Mabinlin Ⅰ和Ⅱ,分子量分别为11.6kD和10.4kD。用Edmail降解和反相HPLC鉴定PTH-aa方法测定证明:二者的N末端均因焦谷氨酸环化而封闭。采用1mol/l HCl-甲醇溶液35℃处理24小时的方法可使之开环。二种蛋白N端肽8个氨基酸残基顺序均为:Pyroglutamic acid-Pro-Arg-Gly-Pro-Ala-Leu-Arg-。羧肽酶酶解的动态分析证明MaI羧端的氨基酸顺序为-Phe-Gln-Leu-Ala-Ser,MaⅡ为-Phe-Gln-Leu-Ala。其差别仅在于MaⅡ缺一个Ser,这一结果表明MaⅠ和MaⅡ的主要差异不是在端肽。     

THE EFFECT OF ORDERED CHARACTERS ON PHYLOGENETIC RECONSTRUCTION

Abstract Morphological structures are likely to undergo more than a single change during the course of evolution. As a result, multistate characters are common in systematic studies and must be dealt with. Particularly interesting is the question of whether or not multistate characters should be treated as ordered (additive) or unordered (non-additive). In accepting a particular hypothesis of order, numerous others are necessarily rejected. We review some of the criteria often used to order character states and the underlying assumptions inherent in these criteria.
The effects that ordered multistate characters can have on phylogenetic reconstruction are examined using 27 data sets. It has been suggested that hypotheses of character state order are more informative then hypotheses of unorder and may restrict the number of equally parsimonious trees as well as increase tree resolution. Our results indicate that ordered characters can produce more, equal or less equally parsimonious trees and can increase, decrease or have no effect on tree resolution. The effect on tree resolution can be a simple gain in resolution or a dramatic change in sister-taxa relationships. In cases where several outgroups are included in the data matrix, hypotheses of order can change character polarities by altering outgroup topology. Ordered characters result in a different topology from unordered characters only when the hierarchy of the cladogram disagrees with the investigator's a priori hypothesis of order. If the best criterion for assessing character evolution is congruence with other characters, the practice of ordering multistate characters is inappropriate.     

COMPARTMENTATION OF AMINO ACID METABOLISM IN THE RAT POSTERIOR PITUITARY

—Isolated rat posterior pituitary glands were incubated with [¹⁴C]glucose or [¹⁴C]acetate and the incorporation of radioactivity into several amino acids was followed. The results indicated that radioactivity was incorporated from [¹⁴C]glucose into a large pool of glutamate which appeared to be responsible for a large proportion of GABA synthesis in the gland. The specific activity of glutamine was always less than that of glutamate when [¹⁴C]glucose was the precursor employed, whereas [¹⁴C]acetate labelled a glutamate pool which had approximately the same specific activity as that of glutamine. The results are discussed with reference to the compartmentation of amino acid metabolism in the nervous system.     

PHYLOGENY OF PRIMATES AND OTHER EUTHERIAN ORDERS: A CLADISTIC ANALYSIS USING AMINO ACID AND NUCLEOTIDE SEQUENCE DATA

Abstract— Genealogical reconstructions carried out by the parsimony method on protein amino acid and DNA nucleotide sequence data are providing fresh evidence on cladistic branching patterns at taxonomic levels from the classes of Vertebrata and orders of Eutheria to the genera of Hominoidea. Minimum length trees constructed from amino acid sequence data group Mammalia with Archosauria (i.e., Aves plus Crocodilia), Amniota with Amphibia, and Tetrapoda with Teleostei. Within Mammalia, Edentata and Paenungulata (e.g., Proboscidea) appear as the most anciently separated from other eutherians. Another superordinal eutherian clade consists of Artiodactyla, Cetacea, and Perissodactyla. A third consistently contains Primates, Lagomorpha, and Tupaia. The cladistic positions of such orders as Carnivora, Chiroptera, Insectivora, and Rodentia are not well resolved by the currently still sparse body of sequence data. However, recent dramatic progress in the technology of gene cloning and nucleotide sequencing has opened the way for so enlarging the body of sequence data that it should become possible to solve almost any problem concerning the phylogenetic systematice of extant mammals. An example is provided by hominoid genera. Minimum length trees constructed from mitochondrial DNA nucleotide sequence data very strongly group Pan, Homo , and Gorilla into Homininae and then join Homininae and Ponginae (pongo) into Hominidae as the sister family of Hylobatidae (Hylobates). Resolution of the hominine trichotomy into two dichotomous branchings should be forthcoming as kilobase sequencing of nuclear genes progresses.     

上海郊区黑斑蛙皮中两个新肽的分离和结构鉴定

<正> 黑斑蚌(Rana nigromaculata)皮的甲醇提取物经碱性氧化铝层析,所得50％乙醇洗脱液冻干后用反相HPLC分离得到18组峰。其中第9—10组峰与第15组峰进一步统化得9-10-10(Fig.1)与15-5-2(Fig.2)。按文献方法所得氨基酸组成分析结果分别是:     

氨基酸残基无序排列对蛋白质分子电子能谱的影响

我们用Dean负因子计数方法计算了氨基酸残基无序排列的蛋白质分子的电子能谱。结果表明当含有较多种氨基酸时,无序蛋白质分子的价带很宽,这样价带中的空穴就有很大的迁移率。     

THE RELATIONSHIP BETWEEN AMINO ACID INCORPORATION INTO PROTEIN IN ISOLATED NEOCORTEX SLICES AND THE TISSUE CONTENT OF FREE AMINO ACID

Abstract— The uptake of radioactive leucine by incubated neocortex slices was found to be increased by electrical stimulation, yielding a higher content of radioactive amino acid per g fresh weight of tissue which was maintained for prolonged periods of stimulation. The increased tissue content may be associated with tissue swelling found on electrical stimulation, but the additional amino acid uptake was by an active process rather than by passive diffusion. Additions of valine (2.5–10 m m ) or tryptophan (1 m m ) to the incubation medium was found to depress the tissue leucine content. Decreasing the tissue free leucine content by incubating slices in medium containing 5 m m -valine was found to decrease the incorporation of leucine and lysine into tissue protein, indicating that under these conditions tissue free amino acid becomes rate limiting for amino acid incorporation into protein. By analogy with the properties of cerebral tissue in oitro it is suggested that electrical activity in vivo may cause localized increases in free amino acid concentration which may serve to regulate protein synthesis in conditions where the concentration of free amino acids are rate limiting.     

THE EFFECT OF DELTA-AMINOLAEVULINIC ACID ON THE UPTAKE AND EFFLUX OF AMINO ACID NEUROTRANSMITTERS IN RAT BRAIN SYNAPTOSOMES

Abstract— δ-Aminolaevulinic acid (δ-ALA) is an omega amino acid structurally similar to γ-aminobutyric acid (GABA) and l -glutamate. We have examined the effect of δ-ALA on the uptake and efflux of radiolabelled GABA and l -glutamate in rat cortical synaptosomes and report: (1) low concentrations of δ-ALA reduced the potassium-stimulated release of [³H]GABA from the synaptosome preparation. This effect was reversed by the GABA receptor antagonist bicuculline. We postulate that GABA release is modulated by a feedback mechanism on presynaptic GABA receptors, and that δ-ALA has agonist activity at these receptors. (2) δ-ALA at high concentrations (0.75-5.0 m m ) stimulated the efflux of l -[¹⁴C]glutamate from preloaded synaptosomes. (3) δ-ALA had no effect on potassium-stimulated release of l -glutamate. (4) Uptake of labelled l -glutamate was inhibited by δ-ALA in a noncompetitive fashion. (5) Synaptosomes did not accumulate [¹⁴C]δ-ALA in the range 0.5-50 δ m . These results are discussed in relation to the control of GABA release from nerve endings, and the role of δ-ALA in the neuropsychiatric manifestations of the acute porphyric attack.     

AMINO ACID SEQUENCE ANALYSIS OF THE SMALL SUBUNIT OF RIBULOSE BISPHOSPHATE CARBOXYLASE FROM FUCUS (PHAEOPHYCEAE)1

This paper reports for the first time amino acid sequence information for the small subunit of ribulose-1,5-bisphosphate carboxylase / oxygenase (Rubisco) from a non-green alga. N-terminal sequences are presented for the polypeptide from three species of the genus Fucus (Phaeophyceae). Although homologous to small subunit polypeptides from other organisms, the Fucus sequences exhibit a unique N-terminal section resembling neither cyanobacterial nor chlorophytic sequences. This difference may be a consequence of the plastid DNA coding arrangement for the small subunit in chromophytes, a situation reported for the related organism Olisthodiscus but not previously investigated at the amino acid sequence level.     

脱共生作用对黑豆蚜氨基酸代谢的影响(英文)

为了解共生菌对黑豆蚜蛋白质、氨基酸代谢的影响 ,用利福平处理黑豆蚜以除去其细胞内共生细菌 ,产生脱共生蚜虫。结果表明 ,被脱去共生菌的蚜虫与未经抗生素处理的正常蚜虫相比 ,7日龄时 ,脱共生蚜虫每毫克鲜重的总蛋白含量降低了 2 9% ,每毫克鲜重的游离氨基酸含量提高了 17%。对黑豆蚜取食的蚕豆苗韧皮部组织中必需氨基酸所占的比例进行分析后发现 ,蚕豆苗韧皮部组织中的必需氨基酸含量仅占 2 0 % ,而有共生菌的黑豆蚜组织中必需氨基酸已达到 4 4% ,脱共生后降低到 37% ,这些结果证明了黑豆蚜的胞内共生菌为其寄主提供了部分必需氨基酸。通过对游离氨基酸组成的分析发现 ,在测定的 17种氨基酸中 ,必需氨基酸中的苏氨酸在共生蚜虫中所占的比例为 2 1 6 % ,在脱共生蚜虫中仅为 16 7%。同样 ,非必需氨基酸中的酪氨酸和丝氨酸 ,在共生蚜虫中分别占总游离氨基酸的 8 9%和 5 6 % ,而在脱共生蚜虫中却分别升高到 2 1 1%和 13 6 %。这些结果表明 ,各种氨基酸比例的失调 ,造成了脱共生蚜虫蛋白质合成受阻和部分游离氨基酸的积累 ,并因此导致蚜虫发育和繁殖的失调。     

THE ROLE OF BACTERIAL SYMBIONTS IN AMINO ACID COMPOSITION OF BLACK BEAN APHIDS

To evaluate the role of bacterial symbionts ( Buchnera spp. ) in the black bean aphids ( Aphis craccivora Koch), the aphids were treated with the antibiotic, rifampicin, to eliminate their intracellular symbiotic bacteria. Analysis of protein and amino acid concentration in 7-day-old of aposymbiotic aphids showed that the total protein content per mg fresh weight was significantly reduced by 29 %, but free amino acid titers were increased by 17% . The ratio of the essential amino acids was in general only around 20% essential amino acids in phloem sap of broad bean, whereas it was 44% and 37% in symbiotic and aposymbiotic aphids, respectively,suggesting that the composition of the free amino acids was unbalanced. For example, the essential amino acid,threonine represented 21. 6% of essential amino acids in symbiotic aphids, but it was only 16.7% in aposymbiotic aphids. Likewise, two nonessential amino acids, tyrosine and serine, represented 8.9% and 5.6% of total amino acids in symbiontic aphids, respectively, but they enhanced to 21.1% and 13.6% in aposymbiotic aphids. It seems likely that the elevated free amino acid concentration in aposymbiotic aphids was caused by the limited protein anabolism as the result of the unbalanced amino acid composition.     

THE ROLE OF BACTERIAL SYMBIONTS IN AMINO ACID COMPOSITION OF BLACK BEAN APHIDS

To evaluate the role of bacterial symbionts (Buchnera spp.) in the black bean aphids (Aphis craccivora Koch), the aphids were treated with the antibiotic, rifampicin, to eliminate their intracellular symbiotic bacteria. Analysis of protein and amino acid concentration in 7‐day‐old of aposymbiotic aphids showed that the total protein content per mg fresh weight was significantly reduced by 29%, but free amino acid titers were increased by 17%. The ratio of the essential amino acids was in general only around 20% essential amino acids in phloem sap of broad bean, whereas it was 44% and 37% in symbiotic and aposymbiotic aphids, respectively, suggesting that the composition of the free amino acids was unbalanced. For example, the essential amino acid, threonine represented 21.6% of essential amino acids in symbiotic aphids, but it was only 16.7% in aposymbiotic aphids. Likewise, two nonessential amino acids, tyrosine and serine, represented 8.9% and 5.6% of total amino acids in symbiontic aphids, respectively, but they enhanced to 21.1% and 13.6% in aposymbiotic aphids. It seems likely that the elevated free amino acid concentration in aposymbiotic aphids was caused by the limited protein anabolism as the result of the unbalanced amino acid composition.     

系统发育研究中多重序列比对常见问题分析

在简单介绍序列比对原理的基础上,结合自己的经验,对经常出现的问题进行总结分析,以期在将来的序列比对工作中避免此类问题的发生.     

EFFECT OF UNDERNUTRITION ON AMINO ACID COMPARTMENTATION IN THE DEVELOPING RAT BRAIN

—Rat pups undernourished through 21 days of age show abnormal patterns of cerebral amino acid metabolism. The pattern of incorporation of radioactivity from l -[U-¹⁴C]leucine into amino acids derived from tricarboxylic acid cycle intermediates was altered, with significantly more ¹⁴C being incorporated into glutamate and aspartate in the underfed rats than in controls. Glutamate compartmentation, manifested in the ratio of specific radioactivities of glutamine to glutamate, developed more slowly in the. diet-restricted group. These results are similar to those seen in neonatally-thyroidectomized rats and suggest decreased growth of neuronal processes. This impairment of amino acid metabolism returns to normal after a 7-week period of adequate nutrition.