BioMed Central Blog
From the Rhine to the Rift Valley: Human population genetics in Genome Biology
Has hypoxia adaptation in the Ethiopian highlands mirrored that seen in Tibet and the Andes? Is there a genetic definition for an Ashkenazi Jew? These are two questions on human diversity that can now be answered, thanks to new research articles published in this month's Genome Biology.
In the first article, the University of Pennsylvania's Tishkoff lab, in collaboration with Addis Ababa University, sought to identify genetic adaptations to high altitude present in the Amhara people of the Ethiopian Highlands. Two other high altitude populations – in Tibet and the Andes – have previously been studied in this way; obtaining Ethiopian samples, however, proved to be a challenging feat.
A set of strong candidate genes for high altitude selection were identified in the Amhara, whose samples were used both for genotyping and for physiological measurements. As with Tibetan and Andean populations, adaptations targeted the HIF-1 pathway, demonstrating the selective pressure brought about by the risk of hypoxia in high altitude environments. While the three populations share an adaptive pathway in common, the individual genetic changes underlying the hypoxia-resistant phenotype were different in the Ethiopian cohort to that seen in Tibetans or Andeans. This example of convergent evolution suggests that the HIF-1 pathway is an inevitable adaptation for any population under selection pressure for hypoxia.
The definition of what constitutes a Jew is an age-old question without a simple answer. The Ashkenazim are a subpopulation of the Jewish people descended from a small founder population based in Western Europe approximately 1,000 years ago; using the largest Ashkenazi genotyping cohort to date, Todd Lencz (The Feinstein Institute for Medical Research) and colleagues were able to determine a distinct genetic signature that can identify Ashkenazi Jews.
Consistent with previous reports, the article concludes that the founding Ashkenazi population likely included both Levantine Jewish and European Caucasian individuals. However, the results presented by Lencz and colleagues powerfully show that, since the founding event, the level of admixture with "host" European populations (and with other Jewish populations) has been extremely low.
The genetic signature also harbors an enrichment of genes associated with disease pathways known to be overrepresented in the Ashkenazi population, and so will therefore help to unravel the genetic basis by which these conditions (including cystic fibrosis and Usher syndrome) have become prevalent among Ashkenazim.
Posted by Naomi Attar at 13:35 Comments (0)
Aquatic Biosystems: Riding the wave
Aquatic Biosystems, previously Saline Systems, was relaunched today with a broader scope to incorporate all aspects of basic and 
applied research on aquatic organisms and environments.
The first articles published today in Aquatic Biosystems include research by Patricia Assuncao et al. on the molecular taxonomy of new strains of Dunaliella, and research by Steve Ferguson and colleagues on predation behaviour and feeding ecology of killer whales in the Canadian Arctic based on traditional Inuit ecological knowledge and scientific observations.
The new journal also has an expanded Editorial Board, who cover new subject areas including fisheries, microbial ecology, population genetics, and aquatic invertebrate ecology. The journal is ideally placed to benefit from the increasing focus on aquatic biological systems within the scientific community and will be key in disseminating the important research results and information published within this field.
Also published in the journal today is an introductory editorial from Editors-in-Chief Shiladitya DasSarma and Edward Phlips, who discuss the changes in aquatic biological systems through time and the timeliness of Aquatic Biosystems’ relaunch.
“The increasing and widening threats posed by the actions of human biosystems to the integrity and sustainability of aquatic biosystems highlight the importance of understanding how these systems function, and their resilience to environmental change. Understanding the aquatic microbial community and its effects on plants and animals is key to choosing a sustainable future. The complexity of this task will require the use of all available resources, including the wide range of technological capabilities driving basic and applied research in the 21st century.”
We look forward to highlighting other leading articles on aquatic biosystems in the future and to you helping us grow and cement the journals’ reputation in the field as the home for all research on aquatic organisms and environments.
Posted by Genevieve Horne at 14:18 Comments (0)
Bacterial symbionts – the key to fighting pests and diseases?
Arthropods such as insects can be devastatingly efficient pests and disease vectors, posing significant challenges to the agricultural and medical communities. Pesticides used to be a common solution to dealing with pests but, with more stringent environmental regulations on pesticides and increasing pest resistance to the chemicals, new solutions are required.
Many arthropods have evolved a symbiotic relationship with bacteria and this association could potentially be exploited to control pests and disease vectors. This biological control approach, called symbiont-based control strategies, would be preferable to chemical controls due to their lower environmental impact.
In order to exploit the arthropod- bacterial symbiosis, more knowledge of the relationship is required. BMC Microbiology has published a supplement – Arthropod symbiosis: from fundamental studies to pest and disease management consisting of the latest interdisciplinary research in this field. The articles in the supplement look at bacterial symbiosis with pests such as the Anopheles mosquito that spreads malaria, tsetse fly that spreads sleeping sickness and the cereal weevil that devastates cereal crops.
Currently in their initial stages of development, symbiont-based control strategies have the potential to increase global health and food resources by removing arthropod disease vectors and agricultural pests.
Posted by Srimathy Sriskantharajah at 15:12 Comments (0)
Genome Biology special issue on epigenomics
To showcase the exciting developments currently being made in the study of epigenomes, Genome Biology will publish a special issue on epigenomics in the late summer of 2012.
A call for papers has now been issued inviting Research, Method and Software submissions on topics including:
- methylomes (and hydroxymethylomes)
- histone modifications
- nucleosome positioning
- higher order chromatin structure
- genome-interacting non-coding RNAs
If you would like to enquire about the suitability of a manuscript for consideration, please email editorial@genomebiology.com. Potential submissions can also be discussed in person at the "Epigenomics and Chromatin Dynamics" and "Nuclear Events in Plant Gene Expression and Signaling" Keystone Symposia; if you are attending one of these conferences and would like to meet us, then please do get in touch.
Posted by Naomi Attar at 18:38 Comments (0)
Where did the nervous system come from?
As a crucial element to the success of the metazoans, the nervous system represents an important evolutionary development. By studying the most ancient definitive nervous systems present in basal metazoans, Simmons et al aim to uncover the evolutionary origins of the neural cell type.
Today, in EvoDevo, the results of Simmons et al’s study into the genome of the ctenophore Mnemiopsis leidyi, provide insights into the patterning of sensory cells. Mark Martindale, one of the authors, explains ‘By probing the full genome of Mnemiopsis leidyi, we found that it has a genetic complement of LIM homeobox (Lhx) gene neural transcription factor su
bfamilies more similar to that of the sponge (which do not possess neurons) lineage than to the complete repertoire found in placozoans, cnidarians, and bilaterians, providing further evidence for the basal position of ctenophore and sponge lineages relative to Parahoxazoans (Placozoa, Cnidaria, Bilaterian).’
The results suggest that Lhx genes are likely to play a role in the patterning of sensory cells in the ancestor of sponges and ctenophores. Martindale concludes that the evidence ‘suggests that Lhx genes play a combinatorial role in sensory cell fate specification in both ctenophores and sponges and support an hypothesis that neurons evolved from primitive sensory cells’.
Posted by Rhiannon Meaden at 10:33 Comments (0)
BMC Ecology starts 2012 on a high!
The year 20
11 was a successful one for BMC Ecology and 2012 is off to an excellent start with the news that the journal has been accepted for tracking by Thomson Reuters and will receive its first Impact Factor in 2015. We are delighted with this result as it reflects the growth and increased visibility of the journal in its field and the hard work and support given by our Editorial Board and in-house team.
To support and drive the further growth of BMC Ecology, we are now working with external Section Editors on the journal and are pleased to welcome Nick Royle, Josef Settele, Jean Clobert, Michel Baguette, and Mike Bonsall to the journal in these roles. We look forward to working with them on developing their sections in the future and benefiting from their experience and expertise.
In addition to these successes BMC Ecology celebrated the 2011 UN Year of Forests with the publication of a th
ematic series entitled ‘Forests: Looking to the Future’ in conjunction with another of BioMed Central’s open access journals, Carbon Balance and Management. The series published a number of articles, including a review by Raf Aerts and one of BMC Ecology’s Associate Editors Olivier Honnay on forest restoration, which has been highly accessed, and an article by Tiina Sarkinen and colleagues on the effective mapping of dry forest biomes. The series has generated a lot of interest and we are pleased with the promotion that has given the journal, in particular the coverage on Twitter at the Forests 2011 conference in Belgium which was happening at the same time.
We are looking forward to what the rest of 2012 brings.
Posted by Genevieve Horne at 15:33 Comments (0)
Making the most of DNA databases
The Combined DNA Index System (CODIS) was established by the FBI to hold genetic records with the intention of creating investigative leads. Since genetic catalogs such as this were first introduced to the criminal justice system, these databases have seen an enormous amount of growth, with CODIS for example now holding more than 10 million profiles.
In research published in Investigative Genetics today, Budowle et al evaluate the performance of the current CODIS core loci and newly proposed additions through simplified analyses for adventitious hit rates. Dr Budowle further explains their research; ‘we were motivated to carry out this research because of the consequences that can occur with the selection of core genetic markers for forensic DNA databases. It is not a trivial issue and more thought and effort are needed than has been dedicated. Considerations include genetic typing performance, the service to be provided, and the cost to the public. We hope that our paper will motivate the decision makers for selecting an updated core set of markers for CODIS, and for that matter any other forensic DNA database, to draw on a greater breadth of scientific and statistical talent and perform more in depth analyses. We all want a high quality and high performance system that will serve the needs of protecting society’.
The study suggests that the current core loci are not sufficient in meeting present demands, and that at least 19 autosomal loci, or the inclusion of Y chromosome STR loci would be required for CODIS to function effectively. Whilst this research does not claim to provide the solution to managing the CODIS core loci, by highlighting the different options open to improving CODIS through simple examples, it demonstrates the requirement for more comprehensive research to be conducted before recommendations can be followed.
Posted by Rhiannon Meaden at 11:06 Comments (0)
Did parasites evolve thanks to arrested development?
The evolution of complex traits and life history strategies can often involve the process of preadaptation, through which the evolution of a novel trait is facilitated by an existing feature which previously fulfilled a different role. These features can cover a multitude of anatomical, physiological and behavioral adaptations which include physical characteristics as well as intricate mechanisms and pathways.
Stasiuk et al present research in EvoDevo this week surrounding the use of a preadaptive feature in the evolution of parasitism in nematode worms. Nematode parasitism has been speculated to have evolved via a preadaptive mechanism due to the probable high number of evolutionary events leading to parasitism within the group. Furthermore, these events have occurred in species which are interspersed with non-parasitic species, and therefore, all parasitic species in the group cannot be united through a single common parasitic ancestor.
In order to test this theory, and their own hypothesis that the dauer larva (a developmentally arrested morph of many free living nematodes, likely to have been present in the last common ancestor to nematodes) represents a possible preadaptation to parasitism, Stasiuk et al discuss a series of experiments into the facultative development of either parasitic or free living life-cycles. They compare life history strategies of Caenorhabditis elegans, a free living nematode with dauer stage larva, and Parastrongyloides trichosuri, a nemataode which uses both parasitic and free living life history strategies, dependent on environmental cues.
The authors conclude that their experiments do indeed support the hypothesis of the evolution of parasitism in P.trichosuri through a preadapted developmentally arrested life stage similar to that of the dauer larva in C.elegans. They show that similar environmental cues such as temperature, population density and food availability may affect the formation of dauer larva in C.elegans and uptake of a parasitic life mode in P.trichosuri.
Posted by Rhiannon Meaden at 11:00 Comments (0)
Genome Biology publishes MiSeq data
The pioneering genomicist Sydney Brenner has a sound bite that the most important -omics discipline of all is econ-omics.
The holy grail of biomedical research is to translate scientific achievement into practical applications in the clinic. And for genomics to conquer the local hospital ward, it must not only be genom-ical – but also econ-omical.
2011 has seen economical genomics arrive one step closer with the unveiling of two sequencing machines of note that are designed to be affordable to small operations: Illumina's MiSeq and Life Technologies' Ion Torrent Personal Genome Machine.
A new article published in Genome Biology by Olivier Harismendy, Kelly Frazer and colleagues is one of the first publications to showcase MiSeq data. The focus of the article is an ultra-deep targeted sequencing method ('UDT-seq') for the detection of low prevalence mutations in heterogeneous tumor samples. In the article, the authors use calibrated human DNA samples to demonstrate the superior performance of MiSeq over Illumina's Genome Analyzer II platform, in terms of both sensitivity and speed.
The impressive quality of the data generated by MiSeq is an encouraging sign that routine sequencing in the clinic may soon become a reality, and that a new era of radically different diagnosis and pharmacology stratagies may be just around the corner.
As with all sequencing data described in Genome Biology articles, the MiSeq data are available in a public repository (NBCI SRA: SRP009487). The MiSeq vs GAII comparison is also nicely complemented by last month’s article from Heinz Himmelbauer and colleagues, which compared the errors and biases in GAII and Illumina HiSeq datasets.
Posted by Naomi Attar at 11:45 Comments (0)
Abnormalities in brain circuitry as a cause of depression
As a highly variable and debilitating disease, major depressive disorder (MDD) can be notoriously difficult to treat. Many of the difficulties associated with establishing an effective treatment program for those affected by MDD stem from a lack of understanding of the underlying biology of the disorder. The biological basis of mood disorders is a rapidly advancing field, and there is hope that over the next few years, knowledge gained in this area will help advance clinical therapy.
Published in Biology of Mood & Anxiety Disorders this week, Furman et al. present findings from recent research using functional magnetic resonance imaging (fMRI) to compare the brain circuitry of participants diagnosed with MDD and a control group of individuals with no history of psychiatric disorder. Based on the findings from previous work, they focus their research on frontostriatal functional connectivity. Their results suggest that there may be a link between aberrant connectivity and MDD, whereby depressed individuals display attenuated functional connectivity between the ventral striatum and both ventromedial prefrontal cortex and subgenual anterior cingulate cortex.
This study highlights the need for further research to explicitly examine links between mood disorders and connectivity, in particular with regard to specific symptoms. Studies such as this indicate that the management of mood disorders could evolve over time to focus on symptom-specific, targeted treatment, based on the biological root of the disorder.
Posted by Rhiannon Meaden at 12:30 Comments (0)
Dystrophin/dysferlin null mice as useful therapeutic models
It is well known that some
forms of muscular
dystrophies are caused by mutations in the genes coding for dystrophin and
dysferlin – two proteins which both have important roles in the correct
functioning of skeletal muscle.
The dystrophin protein is located in the plasma membrane of skeletal muscle, and is an integral part of the dystrophin-glycoprotein complex (DGC). The DGC forms a link between the sarcolemma (the muscle cell membrane) and the cytoskeleton thereby ensuring cell membrane stability and preventing damage during lengthening contractions of the muscle. Dysferlin on the other hand is known to play a critical role in calcium dependent membrane repair. A defect in either protein’s role has a detrimental effect on the muscle.
A new research article published this month in Skeletal Muscle uses dystrophin/dysferlin double knock-out (DKO) mice to look at how muscle pathology in dysferlin-null mice is exacerbated by an additional dystrophin deficiency. DKO mice show increased histopathology, decreased sarcolemmal integrity and severe functional defects. The double deficiency causes more severe muscular dystrophy than dysferlin-deficient or wild type mice, and also results in the mice being physically weaker, suffering from contraction-induced injuries and having a low force production. In addition, onset of the muscle pathology in mice lacking both dystrophin and dysferlin is earlier than in the dysferlin-deficient mice.
Han et al. reveal that the role dysferlin has in repairing damaged membranes can be unmasked by a dystrophin deficiency. In dystrophin deficient mice, the initial injury caused by lengthening muscle contractions is more severe than in wild type and dysferlin-null mice. Dystrophin deficient mice are however capable of recovery, revealing the presence of an active membrane repair process to restore membrane integrity. Dysferlin mice on the other hand show a poor recovery, as do DKO mice. These results suggest that the DKO mouse model may be useful in the development of therapies designed to treat dysferlinopathies – muscular dystrophies caused by a defect in the function of the dysferlin protein.
To keep up to date with the latest articles from Skeletal Muscle, why not visit our homepage and register to receive article alerts?
Posted by Laura Winton at 16:09 Comments (0)
Christmas comments from ‘Mark my words’
Mark Jobling, a welcome trust senior research fellow, and professor of genetics at Leicester University, presents a series of short commentaries published in Investigative Genetics every two months. His column provides a thoughtful discussion of the world of genetics, across a varied range of topics- reflecting the wide scope of the journal.
In this month’s ‘Mark my words’ column, Mark struggles with finding an appropriately seasonal topic on which to discuss the topic of genetics. His pondering of the possible topics suggested by PubMed provides him with little inspiration, as articles brought up are almost satirical in their discussions of the dangers of the Christmas period and all things festive.
His musings on possible Christmas wish-lists, and the overwhelmingly Apple dominated world of electronics lead him to hit upon a topic which he was asked to discuss at a decidedly Apple-free Café Scientifique- where technology such as powerpoints is not encouraged in presentations. And so, Mark has found an equally Christmassy and genetically relevant topic of virgin birth- or parthenogenesis.
Parthenogenesis is not an uncommon form of reproduction among certain members of the animal kingdom, and indeed provides the greatest genetic pay-off for the investment of resources by the mother-from a selfish perspective. However, as Mark points out, the high price of asexual reproduction in the form of genetic uniformity (and therefore increased susceptibility to pathogens) can explain why sexual reproduction is almost uniform- with many asexual species being transient. Using an example of a child who was thought to be of parthenogenetic origin (but in fact turned out to be a chimaera) Mark demonstrates that, for humans at least, this mode of reproduction is not viable- even at Christmas. So, Mark’s discussion leads us to conclude that a virgin-birth would indeed be a miracle!
Posted by Rhiannon Meaden at 10:09 Comments (0)
EvoDevo: can cytasters shed light on eumetazoan phylogeny?
Cytasters (or cytoplasmic asters) can be found in the cortical cytoplasm of the bilaterian egg and zygote; they are centriole-based nucleation centers of microtubule polymerization. Cytasters play an important role in development, and are thought to be responsible for the organization of the ectoplasmic domain where networks of connected cytasters form the cortical microtubule cytoskeleton in the ectoplasm.
Salinas-Saavedra and Vargas propose a novel hypothesis in EvoDevo today regarding the conservation of cytasters as a homologous feature, found in Bilateria and already present the common ancestor to both protostomes and deuterostomes. They collate and compare published evidence from numerous studies, identifying an almost unanimous trend for the presence of cytasters in bilaterian species (with notable differences discussed in mice, rabbits and cows). The authors propose that the similarities in the development of cytasters seen across the majority of the studied species suggest that this trait is conserved and evolutionarily ancient, and thus support the hypothesis of a homologous rather than homoplasic origin of cytasters.
Cortical cytasters: A highly conserved developmental trait of Bilateria with similarities to Ctenophora
Miguel Salinas-Saavedra, Alexander O Vargas EvoDevo 2011, 2:23 (1 December 2011)
Abstract | Provisional PDF
Further research is needed across a number of unrepresented phyla, to which this hypothesis was unable to draw conclusions regarding in identifying cytasters. The authors feel that there is strong support for homology of cytasters, citing the absence of these (as seen in cows) as a secondary loss. Further evidence is required in a number of phyla, for which there was no published research deciding on the presence of absence of cytasters, in order to explore this theory further.
Posted by Rhiannon Meaden at 12:34 Comments (0)
New thematic series to highlight the end of 2011 - UN Year of Forests
2011 has been the UN International Year of Forests and to highlight this, two of BioMed Central’s open access journals, BMC Ecology and Carbon Balance and Management, have joined forces to create a thematic series showcasing the latest research into these crucial ecosystems.
The two journals’ differing scopes are reflected in the different research themes highlighted in the series. Co Editor-in-Chief of Carbon Balance and Management, Georgii Alexandrov, introduces the thematic series in his editorial and discusses the importance of Land-Use/Land-Cover Change models in setting forest conservation targets. In a separate article, BMC Ecology’s Associate Editor Olivier Honnay reviews the use of a biodiversity-ecosystem functioning perspective in forest restoration. This approach, and its emphasis on functional rather than taxonomic diversity, may lead to a more pragmatic approach to forest restoration where a species’ function, rather than its origin, is assessed when selecting tree species to include.
Non-native tree species are also discussed in research by Annabel J Porte and colleagues who studied the invasive maple species, Acer negundo, which displays higher phenotypic plasticity than native species under non-limiting resource environments, explaining how these trees are able to spread throughout the resource rich forests of Europe.
Further articles published by Carbon Balance and Management in the thematic series include research by Dr Grant Domke et al. on the importance of incorporating density reductions and structural loss adjustments when assessing forest biomass and carbon stock estimates, and a timely review by Dr Martin Herold et al. discussing the best options for monitoring past carbon emissions from forest degradation.
Finally, BMC Ecology presents research by Tiina Särkinen and colleagues on the seasonally dry tropical forests (SDTF) of South America. Current biome maps for these areas vary considerably and highlight the difficulty in mapping highly discontinuous and fragmented vegetation like SDTF over large areas. Potential new methods for modeling these areas are presented with the hope that the generation of more reliable maps will allow further research into these threatened forests.
Over the forthcoming months we will be adding new articles to the series and we hope you enjoy reading them and keeping up to date with developments in this important area of research.
Philippa Harris
Senior Executive Editor
BMC Ecology
Genevieve Horne
Senior Journal Development Editor
BMC Ecology and Carbon Balance and Management
Posted by Genevieve Horne at 14:20 Comments (0)
Technological Insights and Research Highlights in Comparative Genomics
The recent EMBO conference on comparative genomics of eukaryotic microorganisms provided a forum for discussion of some of the biggest and most challenging questions in evolutionary biology. The conference aimed to bring together worldwide experts in the field, and facilitate debate around the current state and future of comparative genomics of eukaryotic organisms.
In a meeting report published in EvoDevo today, Inaki Ruiz-Trillo and Alex de Mendoza convey the key points broached in the conference and highlight areas of interest to the EvoDevo community. They discuss the implications of technological advances (notably in high throughput sequencing) which are allowing rapid sequencing of novel genomes. These new genome sequences have the potential to reveal a range of insights into the emergence of eukaryotic diversity, biology and evolution.
A range of presentations proved to be relevant to evolutionary developmental biologists. Of particular interest were discussions on the use of sub-telomeric regions and the generation of genetic diversity, experimental evolution as a basis to study directional selection, the role of horizontal gene transfer in convergent evolution, new phylogenetic methods in constructing the tree of life, and symposia on mitochondrial genomes and metagenomics.
EvoDevo publishes articles on a broad range of topics associated with the translation of genotype to phenotype in a phylogenetic context. Research, reviews and reports can be submitted via the online submission system and benefit from rapid peer review process and fast publication.
To keep up to date with the latest EvoDevo articles, why not visit our homepage and register to receive article alerts when new research is published?
Posted by Rhiannon Meaden at 10:58 Comments (0)