Molecular Recombination in T4 Bacteriophage Deoxyribonucleic Acid II. Single-Strand Breaks and Exposure of Uncomplemented Areas as a Prerequisite for Recombination

Deoxyribonucleic acid (DNA) from several "DNA-deficient" amber mutants was observed to be either nicked (amber 22, 82, 122, and wild type) or cut (amber 453) after injection into a nonpermissive host. This effect was inhibited by chloramphenicol (CM), indicating that it is due to phage-induced enzymes. Although most of the mutants tested for replication in a density-label system were in fact DNA-deficient (amber 22, 82, 122), one (amber 81) was found to replicate almost identically to the wild type, and another (amber 453) was found to assume a hybrid density only. The hybrid moiety was less than, or equal to, one phage equivalent length, and was more efficiently extracted from infected bacteria than was similarly replicated DNA from wild-type phage. Interparental recombination between heavy and light parental DNA was observed for amber 82, 122, and wild type, but was not observed for amber 453; it was inhibited by CM. In contrast to amber 82 and wild type, the amber 453 intracellular DNA does not have single-strand regions, Because amber 453, unlike amber 82 and wild type T4, does not recombine, nicking and exposure of single-strand regions is postulated to be a prerequisite for recombination.     

Entrapment Bias of Arthropods in Miocene Amber Revealed by Trapping Experiments in a Tropical Forest in Chiapas,Mexico

All entomological traps have a capturing bias, and amber, viewed as a trap, is no exception. Thus the fauna trapped in amber does not represent the total existing fauna of the former amber forest, rather the fauna living in and around the resin producing tree. In this paper we compare arthropods from a forest very similar to the reconstruction of the Miocene Mexican amber forest, and determine the bias of different trapping methods, including amber. We also show, using cluster analyses, measurements of the trapped arthropods, and guild distribution, that the amber trap is a complex entomological trap not comparable with a single artificial trap. At the order level, the most similar trap to amber is the sticky trap. However, in the case of Diptera, at the family level, the Malaise trap is also very similar to amber. Amber captured a higher diversity of arthropods than each of the artificial traps, based on our study of Mexican amber from the Middle Miocene, a time of climate optimum, where temperature and humidity were probably higher than in modern Central America. We conclude that the size bias is qualitatively independent of the kind of trap for non–extreme values. We suggest that frequent specimens in amber were not necessarily the most frequent arthropods in the former amber forest. Selected taxa with higher numbers of specimens appear in amber because of their ecology and behavior, usually closely related with a tree–inhabiting life. Finally, changes of diversity from the Middle Miocene to Recent time in Central and South America can be analyzed by comparing the rich amber faunas from Mexico and the Dominican Republic with the fauna trapped using sticky and Malaise traps in Central America.     

缅甸琥珀内含物形态结构在X射线下的可辨识性

【目的】产自缅甸北部胡康河谷的缅甸琥珀形成于白垩纪中期。其艺术价值很高,同时其内含物的生物多样性程度也很高,故其科学价值也不可估量。显微CT能够提供化石(琥珀)内部解剖结构的高分辨率断层图像,故该方法日渐成为目前琥珀研究中的常用方法之一。然而在可见光下可见的琥珀内的生物结构,在X射线下却有不同的结果,这与现生研究材料在显微CT下的表现非常不同。本研究对产自胡康河谷的9块缅甸琥珀进行显微CT检测,试图对这个特殊的现象进行较为系统的解读。【方法】利用数码相机(Nikon 5200D)拍摄琥珀照片,并用Helicon Focus 5.3软件合成。通过显微CT技术扫描琥珀和计算机断层重建技术重建出缅甸琥珀内含物的三维结构形态。【结果】显微CT检测结果主要分为3种:完全无衬度、部分结构有衬度和整体结构有较好衬度。本研究对有较好衬度的琥珀内含物进行了三维重建,展示了琥珀内含物的外部和内部三维结构。【结论】琥珀内含物的可见光成像和X射线成像不存在一一对应关系,其原因和琥珀保存的好坏以及琥珀的密度差、琥珀围岩之间的对比度差异有关。琥珀形成和埋藏过程中的物理和化学变化非常复杂,其机理的探究也更为复杂和困难,本文对这个现象的主要类型做了较为初步的阐述,后续研究需要更为全面的选样和更为严格的实验设计才能够最终解决这个埋藏学上的难题。     

A new genus and species of gall midges of the supertribe Heteropezidi (Diptera,Cecidomyiidae) found in Eocene amber from Sakhalin

A new genus and species of pedogenetic gall midge, Estoperpetua sakhalinica gen. et sp. nov., of the tribe Heteropezini (subfamily Lasiopterinae) is described. Gall midges have not been recorded in Eocene amber of Sakhalin. A female with 4-segmented tarsi, large transparent triangular sensoria on flagellomeres, short wings and legs, and long 2 + 9-segmented antennae is described. Heteropezidi shows the greatest generic and species diversity in the Late Eocene Rovno amber. Representatives of this supertribe were also found in the Late Eocene Baltic amber, Early Eocene Oise amber, Miocene amber from Mexico and Dominican Republic, and African copal. Heteropezidi from different amber faunas are reviewed.     

Transmission of amber mutants of bacteriophage T4. III. Thermostability of the replication of amber mutants in cells of a non-permissive host is typical for the majority of phage tail genes

The article deals with determination of the spreading of the earlier discovered phenomenon of the temperature sensitivity of multiplication of T4 phage amber mutants. On the basis of the study of the dependence of multiplication of 50 amber mutants in 22 genes of T4 phage tail in the cells of non-permissive host on the incubation temperature in the range of 15-41 degrees C, the following conclusion is drawn: temperature sensitivity of multiplication of amber mutants appears to be gene-specific and is widely spread among T4 phage genes, i.e. in the case of amber mutants the burst size decreases, even for 14 tail genes, by several orders with the increase in incubation temperature. Temperature sensitivity of multiplication is typical of amber mutants in the genes whose proteins are either of small number in a phage particle (several molecules) or play the role of catalytic factors. Moreover, genes, amber mutants of which possess temperature sensitivity of multiplication, map in defined clusters.     

白垩纪中期缅甸琥珀中陆生腹足类化石的新发现

腹足类化石在地层中丰富且常见,但在琥珀中保存较少。文中描述了产自白垩纪中期缅甸琥珀中的陆生腹足类化石2属2种:Euthema naggsi Yu, Wang and Pan, 2018, Truncatellina dilatatus sp. nov.。这些陆生腹足类新材料的发现,提高了缅甸琥珀中陆生腹足类物种多样性,并进一步印证了白垩纪中期缅甸琥珀森林温暖潮湿的热带雨林环境。     

The Range of Bioinclusions and Pseudoinclusions Preserved in a New Turonian (~90 Ma) Amber Occurrence from Southern Australia

A new Turonian amber occurrence, representing the oldest in situ amber locality in Australia and the southern-most locality in Gondwana, has recently been discovered in the Otway Basin of Victoria. The amber was collected from petroleum cores and many pieces contain a range of inclusions that can provide information on the depositional history of the resin. To date, one species of fern spore (Cyathidites minor) and one species of lycophyte spore (Kraeuselisporites sp?) have been conclusively identified in the amber, along with filamentous microorganisms and degraded plant matter. Several samples are also rife with pseudoinclusions as reported recently in other ambers. The abundance of preserved particulate debris and wind dispersed spores suggest that the Otway amber formed subaerially. Furthermore, based on the range of bioinclusions and forms of pseudoinclusions preserved within a single piece of amber, the locus of hardening for individual samples is variably interpreted as occurring in the tree tops, on the tree trunk or on the ground surface. Notably, specific inclusion assemblages are associated with certain colours of amber. By extension, and in accordance with recent studies, amber colour may be indicative of depositional environment. Variation in the environment of solidification may, therefore, be sufficient to account for the broad range of morphological characteristics preserved in a single amber deposit.     

Fossil palm flowers in Dominican and Baltic amber

Five palm flowers in Dominican amber and one in Baltic amber are described or characterized. Palaeoraphe dominicana gen. et sp. nov. in the subtribe Livistoninae, is described from one perfect flower in Dominican amber. Roystonea palaea sp. nov. is described from one staminate and one pistillate flower in Dominican amber. Three other palm flowers, two perfect flowers from Dominican amber and one staminate flower from Baltic amber, are briefly characterized and figured.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 361–367.     

Conditionally lethal amber mutations in the leader peptidase gene of Escherichia coli.

The lep gene of Escherichia coli encodes the leader peptidase which cleaves amino-terminal leader sequences of secreted proteins. To facilitate the study of structure-function relationships of the leader peptidase, 22 amber mutations in lep were isolated by localized mutagenesis. These amber mutants grew at 32 degrees C but not at 42 degrees C in the presence of a temperature-sensitive amber suppressor. Most of them were lethal under sup0 conditions. However, one amber mutant, the lep-9 mutant, exhibited temperature-sensitive growth in the sup0 strain, indicating that the amber fragment is active at 32 degrees C but not at 42 degrees C. Protein precursors of the maltose-binding protein and OmpA accumulate strikingly in the lep-9 mutant.     

Expression of the cloned uvrB gene of Escherichia coli: dependency on nonsense suppressors.

Recombinant plasmid pNP5, consisting of plasmid pMB9 on which the uvrB gene is cloned, fully complements for the defects due to chromosomal uvrB mutations in the presence of the amber suppressor sup-6 or supF. Correndonuclease II activity was also completely restored in in UvrB strains containing both plasmid pNP5 and amber suppressor sup-6, as compared with the parental UvrB+ strain. It is shown that the amber mutation which interferes with the expression of the cloned uvrB gene is located outside this gene. Apparently, the amber mutation exerts a polar effect on uvrB expression that is relieved by sup-6 or supF. Introduction of a rho mutation into suppressor-free UvrB strains, harboring pNP5, did not relieve the polarity caused by the amber mutation.     

Fossil amoebae (Hemiarcherellidae fam. nov.) from Albian (Cretaceous) amber of France

Abstract: Two extraordinarily well‐preserved testate amoebae are described from Late Albian age amber from south‐western France. The specimens are attributed to a new family, the Hemiarcherellidae fam. nov., and are described as Hemiarcherella christellae gen. et sp. nov. The amoebae described herein originate from highly fossiliferous amber pieces. Based on syninclusions, Hemiarcherella christellae was a soil‐dwelling organism, probably an active bacterivore. This taxon represents the third species of testate amoebae described from mid‐Cretaceous French amber. Analysis of this fossil amoeba fauna illustrates the uniqueness of mid‐Cretaceous French amber deposits. Indeed, most amoebae found in amber have been assigned to modern species, corroborating the hypothesis of morphological stasis in different microbial lineages. However, the well‐preserved amoebae fauna found in French amber can be distinguished clearly from modern species and help us to better understand the fossil record of these organisms.     

Terpenoid Compositions and Botanical Origins of Late Cretaceous and Miocene Amber from China

The terpenoid compositions of the Late Cretaceous Xixia amber from Central China and the middle Miocene Zhangpu amber from Southeast China were analyzed by gas chromatography-mass spectrometry (GC-MS) to elucidate their botanical origins. The Xixia amber is characterized by sesquiterpenoids, abietane and phyllocladane type diterpenoids, but lacks phenolic abietanes and labdane derivatives. The molecular compositions indicate that the Xixia amber is most likely contributed by the conifer family Araucariaceae, which is today distributed primarily in the Southern Hemisphere, but widely occurred in the Northern Hemisphere during the Mesozoic according to paleobotanical evidence. The middle Miocene Zhangpu amber is characterized by amyrin and amyrone-based triterpenoids and cadalene-based sesquiterpenoids. It is considered derived from the tropical angiosperm family Dipterocarpaceae based on these compounds and the co-occurring fossil winged fruits of the family in Zhangpu. This provides new evidence for the occurrence of a dipterocarp forest in the middle Miocene of Southeast China. It is the first detailed biomarker study for amber from East Asia.     

Novel amber suppressor tRNAs of mammalian origin.

Two amber suppressor tRNAs have been isolated from calf liver. They are different from previously identified naturally occurring amber suppressors of eukaryotes in so far as they are neither tRNATyr nor tRNAGln. They are leucine iso-acceptors and their nucleotide sequence indicates that they harbour a CAA and a CAG anticodon respectively. Both species are functional as amber suppressors as demonstrated by readthrough of the amber codon which terminates the 126 kd protein gene of tobacco mosaic virus RNA. The results bring new information in the discussion of codon-anticodon recognition and regulation of termination in eukaryotic protein synthesis.     

Ecology and taphonomy of Dominican Republic amber and its inclusions

The taphonomic influences upon fossil faunas are generally assumed to be substantial, but in amber they have been little investigated. By comparing the inclusions in Tertiary amber from the Dominican Republic (Smithsonian Institution's Brodzinsky-Lopez Peña collection) with modern insect populations sampled using various methods and from different habitats, it is possible to test taphonomic hypotheses that bear on interpretations of amber faunas. The biota trapped in amber is here viewed as analogous to modem faunas sampled with man-made traps. Using cluster analysis (Manhattan and Euclidian distance measures -UPGMA clustering algorithm) to compare faunas, the amber-trap fauna is most closely reproduced by present day collection using emergence traps and also shows a strong similarity to the fauna of pitfall trap samples. Faunal dissimilarities indicate that the utility of Dominican Republic amber fossils is limited for ecological studies of the canopy and shrub layers of forests, or of the Orders Coleoptera, Diptera or Hymenoptera. Similarities between modern faunas and the amber fauna allow predictions about the ecological setting of Tertiary amber production: this is indicated as primary rain forest, with regenerating patches of secondary growth, in a low-altitude riparian location. □ Amber, Dominican Republic, Palaeogene, ecology, taphonomy.     

Transmission of amber mutants of bacteriophage T4. IV. The frequency of the phenomenon of temperature sensitivity of replication in non-permissive cells of amber mutants for the head genes

Dependence of multiplication of 42 single and double amber mutants in 16 phage head genes on the incubation temperature was studied in the cells of non-permissive host. For amber mutants in 6 head genes the birst size decreases by several orders, with the increase of the incubation temperature. Among amber mutants of the above mentioned genes, mutants in genes 4 and 65 can be distinguished as those with considerably large burst size at low temperature. Phage head genes form the groups, according to temperature sensitivity of multiplication of amber mutants. These groups, together with corresponding groups of phage tail genes, constitute common temperature-sensitive and non-sensitive gene groups on the phage genomic map.     

Inhibition of hepatitis delta virus RNA editing by short inhibitory RNA-mediated knockdown of ADAR1 but not ADAR2 expression

Hepatitis delta virus (HDV) requires host RNA editing at the viral RNA amber/W site. Of the two host genes responsible for RNA editing via deamination of adenosines in double-stranded RNAs, short inhibitory RNA-mediated knockdown of host ADAR1 expression but not that of ADAR2 led to decreased HDV amber/W editing and virus production. Despite substantial sequence and structural variation among the amber/W sites of the three HDV genotypes, ADAR1a was primarily responsible for editing all three. We conclude that ADAR1 is primarily responsible for editing HDV RNA at the amber/W site during HDV infection.     

Drosophila Nonsense Suppressors: Functional Analysis in Saccharomyces Cerevisiae, Drosophila Tissue Culture Cells and Drosophila Melanogaster

Amber (UAG) and opal (UGA) nonsense suppressors were constructed by oligonucleotide site-directed mutagenesis of two Drosophila melanogaster leucine-tRNA genes and tested in yeast, Drosophila tissue culture cells and transformed flies. Suppression of a variety of amber and opal alleles occurs in yeast. In Drosophila tissue culture cells, the mutant tRNAs suppress hsp70:Adh (alcohol dehydrogenase) amber and opal alleles as well as an hsp70:β-gal (β-galactosidase) amber allele. The mutant tRNAs were also introduced into the Drosophila genome by P element-mediated transformation. No measurable suppression was seen in histochemical assays for Adh(n4) (amber), Adh(nB) (opal), or an amber allele of β-galactosidase. Low levels of suppression (approximately 0.1-0.5% of wild type) were detected using an hsp70:cat (chloramphenicol acetyltransferase) amber mutation. Dominant male sterility was consistently associated with the presence of the amber suppressors.     

Burmese amber: evidence of Gondwanan origin and Cretaceous dispersion

Abstract

Burmese amber is an extremely important source of mid-Cretaceous plant and animal remains with over 870 species of organisms, ranging from protozoa to vertebrates, described from this source. The amber mines are located on the West Burma Block that according to geologists was originally part of Gondwana. The present study introduces some angiosperms and insects in Burmese amber whose closest extant relatives have a Gondwanan distribution and there is no previous evidence of a Laurasian distribution. Based on this evidence, it is proposed that organisms in Burmese amber represent a selection of tropical to subtropical life forms that inhabited the interconnected continents of Gondwana in the Early Cretaceous. Based on the fossil record of angiosperms and their diversity in Burmese amber, the West Burma Block could not have rafted from Gondwana to SE Asia before the Early Cretaceous.     

白垩纪中期缅甸琥珀昆虫行为生态学研究进展

缅甸琥珀生物群产自距今约98.8Ma的白垩纪中期,该生物群是世界上物种多样性很高的琥珀生物群之一,为了解白垩纪中期生物多样性和古生态提供了重要窗口。文中以近年来缅甸琥珀地层学、琥珀生物学研究为依据,总结缅甸琥珀形成环境,并对缅甸琥珀揭示的昆虫与植物的协同演化、昆虫的捕食、社会性证据、寄生、求偶和结构色等方面的研究结果进行总结,以期较全面地综述缅甸琥珀的古环境和昆虫行为生态学特征。