Mycobacterium paratuberculosis zoonosis is a One Health emergency

EcoHealth - A singular pathogen has been killing animals, contaminating food and causing an array of human diseases. Mycobacterium avium subspecies paratuberculosis (MAP) is the cause of a fatal...     

The Darmstadt workshop on molecular modeling: Past and future

The majority of the contributions in this issue of the Journal of Molecular Graphics are papers that were presented at the Seventh Darmstadt Molecular Modeling Workshop, which took place at the Technical University Darmstadt on May 18–19, 1993. The technical organization of this workshop was again in the hands of the physical chemistry staff of the Technical University, Darmstadt, as it has been for the past six years. The scientific program was coordinated by Stefan Kast from the author's research group. The Darmstadt Workshop has been quite an informal and inexpensive event throughout the years. From 1994 onward, it will also be a specific meeting of the recently founded German-speaking branch of the Molecular Graphics Society. The following notes should help to provide an overview of the past activities and present some ideas for the future of this meeting.     

One Health: Past Successes and Future Challenges in Three African Contexts

Background

The recent emergence of zoonotic diseases such as Highly Pathogenic Avian Influenza (HPAI) and Severe Acute Respiratory Syndrome (SARS) have contributed to dominant Global Health narratives around health securitisation and pandemic preparedness, calling for greater co-operation between the health, veterinary and environmental sectors in the ever-evolving One Health movement. A decade later, One Health advocates face increasing pressure to translate the approach from theory into action.

Methodology/Principal Findings

A qualitative case study methodology was used to examine the emerging relationships between international One Health dialogue and its practical implementation in the African health policy context. A series of Key Informant Interviews (n = 32) with policy makers, government officials and academics in Nigeria, Tanzania and Uganda are presented as three separate case studies. Each case examines a significant aspect of One Health operationalisation, framed around the control of both emerging and Neglected Zoonotic Diseases including HPAI, Human African Trypanosomiasis and rabies. The research found that while there is general enthusiasm and a strong affirmative argument for adoption of One Health approaches in Africa, identifying alternative contexts away from a narrow focus on pandemics will help broaden its appeal, particularly for national or regionally significant endemic and neglected diseases not usually addressed under a “global” remit.

Conclusions/Significance

There is no ‘one size fits all’ approach to achieving the intersectoral collaboration, significant resource mobilisation and political co-operation required to realise a One Health approach. Individual country requirements cannot be underestimated, dismissed or prescribed in a top down manner. This article contributes to the growing discussion regarding not whether One Health should be operationalised, but how this may be achieved.     

The Neandertal genome and ancient DNA authenticity

Recent advances in high‐thoughput DNA sequencing have made genome‐scale analyses of genomes of extinct organisms possible. With these new opportunities come new difficulties in assessing the authenticity of the DNA sequences retrieved. We discuss how these difficulties can be addressed, particularly with regard to analyses of the Neandertal genome. We argue that only direct assays of DNA sequence positions in which Neandertals differ from all contemporary humans can serve as a reliable means to estimate human contamination. Indirect measures, such as the extent of DNA fragmentation, nucleotide misincorporations, or comparison of derived allele frequencies in different fragment size classes, are unreliable. Fortunately, interim approaches based on mtDNA differences between Neandertals and current humans, detection of male contamination through Y chromosomal sequences, and repeated sequencing from the same fossil to detect autosomal contamination allow initial large‐scale sequencing of Neandertal genomes. This will result in the discovery of fixed differences in the nuclear genome between Neandertals and current humans that can serve as future direct assays for contamination. For analyses of other fossil hominins, which may become possible in the future, we suggest a similar ‘boot‐strap’ approach in which interim approaches are applied until sufficient data for more definitive direct assays are acquired.     

Paleo‐metagenomics of North American fossil packrat middens: Past biodiversity revealed by ancient DNA

Fossil rodent middens are powerful tools in paleoecology. In arid parts of western North America, packrat (Neotoma spp.) middens preserve plant and animal remains for tens of thousands of years. Midden contents are so well preserved that fragments of endogenous ancient DNA (aDNA) can be extracted and analyzed across millennia. Here, we explore the use of shotgun metagenomics to study the aDNA obtained from packrat middens up to 32,000 C¹⁴ years old. Eleven Illumina HiSeq 2500 libraries were successfully sequenced, and between 0.11% and 6.7% of reads were classified using Centrifuge against the NCBI “nt” database. Eukaryotic taxa identified belonged primarily to vascular plants with smaller proportions mapping to ascomycete fungi, arthropods, chordates, and nematodes. Plant taxonomic diversity in the middens is shown to change through time and tracks changes in assemblages determined by morphological examination of the plant remains. Amplicon sequencing of ITS2 and rbcL provided minimal data for some middens, but failed at amplifying the highly fragmented DNA present in others. With repeated sampling and deep sequencing, analysis of packrat midden aDNA from well‐preserved midden material can provide highly detailed characterizations of past communities of plants, animals, bacteria, and fungi present as trace DNA fossils. The prospects for gaining more paleoecological insights from aDNA for rodent middens will continue to improve with optimization of laboratory methods, decreasing sequencing costs, and increasing computational power.     

Tissue banking for research: connecting the disconnected

Delivering the promise of personalised medicine is the challenge that the current generation of scientists face. The variations in human physiology and disease are considerable, and designing appropriate strategies to deliver what has been promised will require access to tissue from a large number of volunteers. The NHS provides an ideal infrastructure for sample acquisition, but requires two things to make this available—public consent and support for extra manpower and administration. There is a disconnection between the NHS and tissue based research that needs to be addressed on a number of levels to provide a translational platform. This should enable the path to be beaten to provide the ideal tailored treatment for future patients; one that preserves quality of life by curing the disease with minimal side effects.     

European neolithization and ancient DNA: an assessment

Neolithic processes underlying the distribution of genetic diversity among European populations have been the subject of intense debate since the first genetic data became available. However, patterns observed in the current European gene pool are the outcome of Paleolithic and Neolithic processes, overlaid with four millennia of further developments. This observation encouraged paleogeneticists to contribute to the debate by directly comparing genetic variation from the ancient inhabitants of Europe to their contemporary counterparts. Pre-Neolithic and Neolithic paleogenetic data are becoming increasingly available for north and northwest European populations. Despite the numerous problems inherent in the paleogenetic approach, the accumulation of ancient DNA datasets offers new perspectives from which to interpret the interactions between hunter-gatherer and farming communities. In light of information emerging from diverse disciplines, including recent paleogenetic studies, the most plausible model explaining the movement of Neolithic pioneer groups in central Europe is that of leapfrog migration.     

Biological evolution and ancient DNA

Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.     

The ancient lakes of Indonesia: towards integrated research on speciation

Ancient lakes have provided considerable insights into the drivers of speciation and adaptive radiation in aquatic organisms. Most studies of species-flocks, however, focus only on a single group of organisms, and few have attempted to integrate geological, limnological, ecological, and genetic drivers of speciation on multiple species-flocks at various trophic levels. As such, there is a need for a comprehensive model system for research on speciation in aquatic environments where multiple radiations are investigated at various levels of biological organization (e.g., individual, population, and ecosystem) and placed in light of geographical and geological setting. The ancient Malili Lakes of Sulawesi, Indonesia, are ideal candidates for such a model, and represent the only hydrologically connected ancient lakes in the world. These lakes are characterized by ultra-oligotrophy and unique physicochemical conditions that govern the composition and production of planktonic communities. At higher trophic levels, there are three recurring trends: (1) low taxonomic richness and simple community structures, (2) adaptive radiations with trophic specialization, and (3) remarkably high endemism with evolutionary innovations throughout the lakes and species-flocks. Furthermore, the restricted geographic distributions of species-flocks within the Malili Lakes indicate that each lake constitutes a unique environment, and dispersal among lakes is limited, despite close contemporary connectivity. These observations suggest that ecological and evolutionary processes are regulated from the bottom up, and speciation is primarily facilitated by interspecific and intraspecific competition for limited resources. The Malili Lakes represent an outstanding natural model for integrative research into speciation as they offer the opportunity to explore the roles of geography, dispersal, and selection in the radiation of aquatic organisms.     

DNA recovery from ancient tissues: problems and perspectives

The recovery, amplification and sequencing of nucleic acids from ancient smaples opens new possibilities in many different fields, such as anthropology, archeaology, population genetics, animal and plant evolutionary studies, and forensic medicine. The sample processing for DNA extraction and PCR amplification represents the most delicate phase of ancient DNA analysis, with a major impact on the reproducibility and reliability of the results. In this paper some extraction protocols are reviewed and discussed, with particular reference to the removal of the inhibitory substances usually present in extract from ancient tissues. The effect of contamination from extraneous DNA, a possible source of misleading results, is discussed and guidelines to detect and circumvent the problem are given.     

Hidden ancient repeats in DNA: Mapping and quantification

We have shown, in a previous paper, that tandem repeating sequences, especially triplet repeats, play a very important role in gene evolution. This result led to the formulation of the following hypothesis: most of the genomic sequences evolved through everlasting acts of tandem repeat expansions with subsequent accumulation of changes. In order to estimate how much of the observed sequences have the repeat origin we describe the adaptation of a text segmentation algorithm, based on dynamic programming, to the mapping of the ancient expansion events. The algorithm maximizes the segmentation cost, calculated as the similarity of obtained fragments to the putative repeat sequence. In the first application of the algorithm to segmentations of genomic sequences, a significant difference between the natural sequences and the corresponding shuffled sequences is detected. The natural fragments are longer and more similar to the putative repeat sequences. As our analysis shows, the coding sequences allow for repeats only when the size of the repeated words is divisible by three. In contrast, in the non-coding sequences, all repeated word sizes are present. It was estimated, that in Escherichia coli K12 genome, about 35.5% of sequence can be detectably traced to original simple repeat ancestors. The results shed light on the genomic sequence organization, and strongly confirm the hypothesis about the crucial role of triplet expansions in gene origin and evolution.     

The retrieval of ancient human DNA sequences.

DNA was extracted from approximately 600-year-old human remains found at an archaeological site in the southwestern United States, and mtDNA fragments were amplified by PCR. When these fragments were sequenced directly, multiple sequences seemed to be present. From three representative individuals, DNA fragments of different lengths were quantified and short overlapping amplification products cloned. When amplifications started from <40 molecules, clones contained several different sequences. In contrast, when they were initiated by a few thousand molecules, unambiguous and reproducible results were achieved. These results show that more experimental work than is often applied is necessary to ensure that DNA sequences amplified from ancient human remains are authentic. In particular, quantitation of the numbers of amplifiable molecules is a useful tool to determine the role of contaminating contemporary molecules and PCR errors in amplifications from ancient DNA.     

Damage and repair of ancient DNA

Under certain conditions small amounts of DNA can survive for long periods of time and can be used as polymerase chain reaction (PCR) substrates for the study of phylogenetic relationships and population genetics of extinct plants and animals, including hominids. Because of extensive DNA degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes such as extinct horses, cave bears, the marsupial wolf, the moa, and Neanderthal. In the past few years, this technology has been extended to the study of infectious disease in ancient Egyptian and South American mummies, the dietary habits of ancient animals, and agricultural practices and population dynamics of early native Americans. Hence, ancient DNA contains information pertinent to numerous fields of study including evolution, population genetics, ecology, climatology, medicine, archeology, and behavior. The major obstacles to the study of aDNA are its extremely low yield, contamination with modern DNA, and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived from limited sources. In addition, we will present some of our own preliminary and published data on mechanisms of DNA degradation and some speculative thoughts on strategies for repair and restoration of aDNA.     

Mitochondrial DNA and ancient population growth

In recent years, the study of mitochondrial DNA (mtDNA) variation has entered a new phase with an increasing emphasis on interpretations of demographic, rather than phylogenetic, history. Human mtDNA variation fits a “sudden expansion” model, where the human species expanded rapidly in size during the Late Pleistocene. This paper examines the sudden expansion model with the goal of partitioning total mtDNA diversity in contemporary populations into two components—diversity that existed prior to the population expansion and diversity that arose after the expansion. A method is developed for estimating these components. Analysis of mtDNA diversity within selected human populations shows that 64–80% of mtDNA diversity in contemporary populations arose after the expansion, a consequence of a high mutation rate relative to the number of generations since expansion. The basic model is extended to two components of excess diversity in sub-Saharan Africa—differences in population size before the expansion and differences in the timing of expansion. Results suggest that excess sub-Saharan African mtDNA diversity is due to the combined effects of the sub-Saharan African population being larger in size prior to the expansion and expanding earlier. Am J Phys Anthropol 105:1–7, 1998. © 1998 Wiley-Liss, Inc.