Ashwagandha—An ancient Indian drug

Ashwagandha, the root ofWithania somnifera Dunal, is an ancient drug used in India by practitioners of Ayurvedic mediicne and as a household remedy. The drug is now official in the Indian Pharmacopoeia. Results of a survey regarding the cultivation, collection and marketing of this drug are described.     

Are all fishes ancient polyploids?

Euteleost fishes seem to have more copies of many genes than their tetrapod relatives. Three different mechanisms could explain the origin of these 'extra' fish genes. The duplicates may have been produced during a fish-specific genome duplication event. A second explanation is an increased rate of independent gene duplications in fish. A third possibility is that after gene or genome duplication events in the common ancestor of fish and tetrapods, the latter lost more genes. These three hypotheses have been tested by phylogenetic tree reconstruction. Phylogenetic analyses of sequences from human, mouse, chicken, frog (Xenopus laevis), zebrafish (Danio rerio) and pufferfish (Takifugu rubripes) suggest that ray-finned fishes are likely to have undergone a whole genome duplication event between 200 and 450 million years ago. We also comment here on the evolutionary consequences of this ancient genome duplication.     

Mutations induced by ancient DNA extracts?

We have investigated whether some factor in ancient DNA extractsinduces site-specific mutations in modern DNA. We find no evidencefor higher mutation rates when extracts from three differentPleistocene mammals are added to modern DNA than when wateror extraction blanks are added. We also fail to find evidencethat any such factor affects ancient DNA sequences determinedfrom the same extracts. This as well as the patterns of nucleotidesubstitutions seen in DNA sequences determined from hundredsof other specimens leads us to doubt that a previously unknownmutagenic factor can be a general feature of extracts from oldtissues.     

Geologically ancient DNA: fact or artefact?

Studies continue to report ancient DNA sequences and viable microbial cells that are many millions of years old. In this paper we evaluate some of the most extravagant claims of geologically ancient DNA. We conclude that although exciting, the reports suffer from inadequate experimental setup and insufficient authentication of results. Consequently, it remains doubtful whether amplifiable DNA sequences and viable bacteria can survive over geological timescales. To enhance the credibility of future studies and assist in discarding false-positive results, we propose a rigorous set of authentication criteria for work with geologically ancient DNA.     

Palaeoserology – teeth put into ancient plagues and pandemics

Based on archived medical records and evolutionary modelling, a Coronavirus has been hypothesized as root and causative agent of the so-called ‘Russian Flu’ pandemic that surged in 1889–1890. In a Correspondence published in this volume of Microbial Biotechnology, Ramassy and colleagues try to support historical evidence by true experimental data using 'palaeoserology', a novel approach combining archaeology and modern immunological analysis. This Opinion piece tries to weigh arguments how strong such data may be, and where a refinement of methodology might be desirable before textbooks of medical history switch to call the 1890s pandemic ‘Russian Corona’.     

Cyprinotus incongruens (Ostracoda): an ancient asexual?

Although unisexual ostracods are common, their evolutionary history is now known only from inferences gained through examination of the fossil record. Here we use mtDNA, allozyme and genome size analyses to investigate the origins of unisexuality, polyploidy and clonal diversity in the freshwater ostracod Cyprinotus incongruens . Our genetic evidence suggests that transitions to polyploidy have been common in this taxon and may sometimes involve internal genome-fusion events, in contrast to the usual origin of animal polyploids through interspecific hybridization. Both the extent and congruent patterns of allozyme and mtDNA divergence amongst clones of C. incongruens are consistent with its persistence as an asexual taxon for approximately 5 million years. However, the detected patterns of genetic variation might also reflect the origins of this ostracod through a series of independent transitions to asexuality by several closely related ancestral taxa. The results make it clear that efforts to demonstrate the antiquity of asexual taxa, solely from surveys of the extent of genetic divergence among their component lineages, will ordinarily be ambiguous, requiring confirmation through investigations which search the genome for the genetic consequences of long abandoned recombination.     

Nuclear actin: ancient clue to evolution in eukaryotes?

Until recently it was widely accepted that the dynamic cytoskeletal matrix is exclusive to the cytoplasm of eukaryotes, evolving before the emergence of the cell nucleus to enable phagocytosis, cell motility and the sophisticated functioning of the endomembrane system within the cytosol. The discovery of the existence of a prokaryotic cytoskeleton has changed this picture significantly. As a result, the idea has taken shape that the appearance of actin occurred in the very first cell; therefore, the emergence of microfilaments precedes that of the eukaryotic cytoskeleton. The discovery of nuclear actin opened new perspective on the field, suggesting that the nuclear activities of actin reflect the functions of primordial actin-like proteins. In this paper, we review the recent literature to explore the evolutionary origin of nuclear actin. We conclude that both ancient and eukaryotic features of the actin world can be detected in the nucleus today, which supports the idea that the cytoskeleton attained significant eukaryotic innovations before the tandem evolution of the cytoskeleton and nucleus occurred.     

Bacillus DNA in fossil bees: an ancient symbiosis?

We report here the isolation of DNA from abdominal tissue of four extinct stingless bees (Proplebeia dominicana) in Dominican amber, PCR amplification of a 546-bp fragment of the 16S rRNA gene from Bacillus spp., and their corresponding nucleotide sequences. These sequences were used in basic local alignment search tool searches of nonredundant nucleic acid data bases, and the highest scores were obtained with 16S rRNA sequences from Bacillus spp. Phylogenetic inference analysis by the maximum-likelihood method revealed close phylogenetic relationships of the four presumed ancient Bacillus sequences with Bacillus pumilus, B. firmus, B. subtilis, and B. circulans. These four extant Bacillus spp. are commonly isolated from abdominal tissue of stingless bees. The close phylogenetic association of the extracted DNA sequences with these bee colonizers suggests that a similar bee-Bacillus association existed in the extinct species P. dominicana.     

Is a large-scale DNA-based inventory of ancient life possible?

A complete DNA-based inventory of the Earth's present biota using large-scale high-throughput DNA sequencing of signature region(s) (DNA barcoding) is an ambitious proposal rivaling the Human Genome Project. We examine whether this approach will also enable us to assess the past diversity of the earth's biota. To test this, we sequenced the 5' terminus of the mitochondrial cytochrome c oxidase I (COI) gene of individuals belonging to a group of extinct ratite birds, the moa of New Zealand. Moa comprised a large number of taxa that radiated in isolation on this oceanic landmass. Using a phylogenetic approach based on a large data set including protein coding and 12S DNA sequences as well as morphology, we now have precise information about the number of moa species that once existed. We show that each of the moa species detected using this extensive data set has a unique COI barcode(s) and that they all show low levels of within-species COI variation. Consequently, we conclude that COI sequences accurately identify the species discovered using the larger data set. Hence, more generally, this study suggests that DNA barcoding might also help us detect other extinct animal species and that a large-scale inventory of ancient life is possible.     

Mya arenaria — an ancient invader of the North Sea coast

Mya arenaria currently occupies a wide geographical range in the northern hemisphere, on both coasts of the Atlantic as well as on the Pacific east coast. Some authors claim it also occurs on the Pacific west coast. The species originated in the Pacific during the Miocene and was already present on both Atlantic coasts in the Pliocene. However, it died out on the east coasts of the Pacific and the Atlantic during glaciation of the Pleistocene. With the aid of man it was reintroduced to the North Sea some 400–700 years ago and to the East Pacific last century. In the 1960s it was also introduced to the Black Sea.M. arenaria invaded new habitats by different modes: (1) natural range expansion (2) intentional as plantings, (3) unintentional as a ballast species and (4) unintentional as a byproduct of oyster transplants. Properties that may favor its wide range of distribution and invading success are: high fecundity; planktonic dispersal stages and life stages that lend itself to unintentional transport by humans; a broad spectrum of habitat and food preference; tolerance of a wide range of environmental conditions such as salinity and temperature; longevity, and perhaps relatively large size.     

Problems of reproducibility--does geologically ancient DNA survive in amber-preserved insects?

Apparently ancient DNA has been reported from amber-preserved insects many millions of years old. Rigorous attempts to reproduce these DNA sequences from amber- and copal-preserved bees and flies have failed to detect any authentic ancient insect DNA. Lack of reproducibility suggests that DNA does not survive over millions of years even in amber, the most promising of fossil environments.     

Epithelial organization: new perspective on α-catenin from an ancient source

Cadherins and catenins evidently partnered at the dawn of the animal kingdom to enable the first polarized epithelium, and perhaps animal evolution itself. New evidence from a primitive slime mold, however, suggests that α- and β-catenins may have engaged this function independently, long before cadherins arrived on the scene.     

Did an ancient chlamydial endosymbiosis facilitate the establishment of primary plastids?

Background  

Ancient endosymbioses are responsible for the origins of mitochondria and plastids, and they contribute to the divergence of several major eukaryotic groups. Although chlamydiae, a group of obligate intracellular bacteria, are not found in plants, an unexpected number of chlamydial genes are most similar to plant homologs, which, interestingly, often contain a plastid-targeting signal. This observation has prompted several hypotheses, including gene transfer between chlamydiae and plant-related groups and an ancestral relationship between chlamydiae and cyanobacteria.     

Paradoxical polyembryony? Embryonic cloning in an ancient order of marine bryozoans

Prolific polyembryony is reported in few major taxa, but its occurrence has generated theoretical debate on potential conflict between sexual and asexual reproduction. It is, therefore, important to genetically confirm a widely cited inference, based on microscopy, that polyembryony characterizes marine bryozoans of the order Cyclostomata. Microsatellite genotyping of brooded embryos and maternal colonies conclusively demonstrated polyembryony, while genetic variation among broods within colonies indicated outcrossing via water-borne sperm, in the rocky-shore species Crisia denticulata. The characteristically voluminous brood chamber of cyclostomes is judged to be an adaptation linked to larval cloning and hence an indicator of polyembryony. We speculate that although the almost universal occurrence of polyembryony among crown-group Cyclostomata is probably attributable to phylogenetic constraint, adaptive consequences are likely to be significant.     

Partial uracil–DNA–glycosylase treatment for screening of ancient DNA

The challenge of sequencing ancient DNA has led to the development of specialized laboratory protocols that have focused on reducing contamination and maximizing the number of molecules that are extracted from ancient remains. Despite the fact that success in ancient DNA studies is typically obtained by screening many samples to identify a promising subset, ancient DNA protocols have not, in general, focused on reducing the time required to screen samples. We present an adaptation of a popular ancient library preparation method that makes screening more efficient. First, the DNA extract is treated using a protocol that causes characteristic ancient DNA damage to be restricted to the terminal nucleotides, while nearly eliminating it in the interior of the DNA molecules, allowing a single library to be used both to test for ancient DNA authenticity and to carry out population genetic analysis. Second, the DNA molecules are ligated to a unique pair of barcodes, which eliminates undetected cross-contamination from this step onwards. Third, the barcoded library molecules include incomplete adapters of short length that can increase the specificity of hybridization-based genomic target enrichment. The adapters are completed just before sequencing, so the same DNA library can be used in multiple experiments, and the sequences distinguished. We demonstrate this protocol on 60 ancient human samples.     

Alkylresorcinol biosynthesis in plants: New insights from an ancient enzyme family?

Alkylresorcinols are members of an extensive family of bioactive compounds referred to as phenolic lipids, which occur primarily in plants, fungi and bacteria. In plants, alkylresorcinols and their derivatives are thought to serve important roles as phytoanticipins and allelochemicals, although direct evidence for this is still somewhat lacking. Specialized type III polyketide synthases (referred to as ‘alkylresorcinol synthases’), which catalyze the formation of 5-alkylresorcinols using fatty acyl-CoA starter units and malonyl-CoA extender units, have been characterized from several microbial species; however, until very recently little has been known concerning their plant counterparts. Through the use of sorghum and rice EST and genomic data sets, significant inroads have now been made in this regard. Here we provide additional information concerning our recent report on the identification and characterization of alkylresorcinol synthases from Sorghum bicolor and Oryza sativa, as well as a brief consideration of the emergence of this intriguing subfamily of enzymes.Key words: alkylresorcinol, polyketide synthase, alkylresorcinol synthase, phenolic lipid, antifungal