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1.  SubPatCNV: approximate subspace pattern mining for mapping copy-number variations 
BMC Bioinformatics  2015;16(1):16.
Many DNA copy-number variations (CNVs) are known to lead to phenotypic variations and pathogenesis. While CNVs are often only common in a small number of samples in the studied population or patient cohort, previous work has not focused on customized identification of CNV regions that only exhibit in subsets of samples with advanced data mining techniques to reliably answer questions such as “Which are all the chromosomal fragments showing nearly identical deletions or insertions in more than 30% of the individuals?”.
We introduce a tool for mining CNV subspace patterns, namely SubPatCNV, which is capable of identifying all aberrant CNV regions specific to arbitrary sample subsets larger than a support threshold. By design, SubPatCNV is the implementation of a variation of approximate association pattern mining algorithm under a spatial constraint on the positional CNV probe features. In benchmark test, SubPatCNV was applied to identify population specific germline CNVs from four populations of HapMap samples. In experiments on the TCGA ovarian cancer dataset, SubPatCNV discovered many large aberrant CNV events in patient subgroups, and reported regions enriched with cancer relevant genes. In both HapMap data and TCGA data, it was observed that SubPatCNV employs approximate pattern mining to more effectively identify CNV subspace patterns that are consistent within a subgroup from high-density array data.
SubPatCNV available through a unique scalable open-source software tool that provides the flexibility of identifying CNV regions specific to sample subgroups of different sizes from high-density CNV array data.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0426-7) contains supplementary material, which is available to authorized users.
PMCID: PMC4305219  PMID: 25591662
DNA copy-number variations; Approximate pattern mining; HapMap; Cancer
2.  Emergence of West Nile Virus Lineage 2 in Europe: A Review on the Introduction and Spread of a Mosquito-Borne Disease 
West Nile virus (WNV) is transmitted by mosquitoes and causes fever and encephalitis in humans, equines, and occasionally wild birds. The virus was first isolated in sub-Saharan Africa where it is endemic. WNV lineage 1 has been responsible for repeated disease outbreaks in the countries of the Mediterranean basin over the past 50 years. This lineage was also introduced into North America in 1999 causing widespread human, equine, and avian mortality. WNV lineage 2, the first WNV lineage to be isolated, was believed to be restricted to sub-Saharan Africa causing a relatively mild fever in humans. However, in 2004, an investigation in Hungary of a case of encephalitis in a wild goshawk (Accipiter gentiles) resulted in the isolation of WNV lineage 2. During the summer of 2004, and in subsequent years, the virus appeared to spread locally throughout Hungary and into neighboring Austria. Subsequently, WNV lineage 2 emerged in Greece in 2010 and in Italy in 2011, involving outbreaks on the Italian mainland and Sardinia. Further spread through the Balkan countries is also suspected. Whole genome sequencing has confirmed that the virus responsible for the outbreaks in Greece and Italy was almost identical to that isolated in Hungary. However, unlike the outbreaks in Hungary, the burden of disease in Mediterranean countries has fallen upon the human population with numerous cases of West Nile fever and a relatively higher mortality rate than in previous outbreaks. The emergence of WNV lineage 2 in Europe, its over-wintering and subsequent spread over large distances illustrates the repeated threat of emerging mosquito-borne diseases. This article will review the emergence of WNV lineage 2 in Europe; consider the pathways for virus spread and the public health implications for the continent.
PMCID: PMC4258884  PMID: 25538937
West Nile virus; lineage; emergence; encephalitis; Europe
3.  Patient Identification of the Symptomatic Impact of Charcot Marie Tooth Disease Type 1A 
The burden of Charcot Marie Tooth type 1A, the most common inherited peripheral neuropathy, including impact on patient quality of life is not well understood. This study aims to qualitatively describe the range of symptoms associated with Charcot Marie Tooth type 1A and impact on quality of life.
We performed qualitative interviews with 16 adult Charcot Marie Tooth type 1A patients. Each interview was analyzed using a qualitative framework technique to identify and index symptoms by theme.
Sixteen patients provided 656 quotes. One hundred and forty-five symptoms of importance were identified representing 20 symptomatic themes. Symptoms associated with difficulty with mobility and ambulation, specific activity impairment, and emotional distress were the most frequently mentioned.
Multiple symptoms contribute to Charcot Marie Tooth type 1A disease burden, some previously under-recognized. Improved recognition of under-recognized symptoms will optimize patient care and quality of life.
PMCID: PMC3752697  PMID: 23965405
Charcot Marie Tooth disease type 1A; quality of life; symptoms; inherited neuropathies
4.  Mosquito cell lines: history, isolation, availability and application to assess the threat of arboviral transmission in the United Kingdom 
Parasites & Vectors  2014;7(1):382.
Mosquitoes are highly effective vectors for transmission of human and animal pathogens. Understanding the relationship between pathogen and vector is vital in developing strategies to predict and prevent transmission. Cell lines derived from appropriate mosquito hosts provide a relatively simple tool for investigating the interaction between the host and viruses transmitted by mosquitoes. This review provides a brief overview of the development of mosquito cell lines, methods of isolation, their availability and application for investigating insect-virus interactions.
PMCID: PMC4150944  PMID: 25141888
Mosquitoes; Cell lines; Arboviruses; Vector competence
5.  Delayed presentation of a loose body in undisplaced paediatric talar neck fracture 
World Journal of Orthopedics  2014;5(3):398-401.
Fractures of the talus are rare in children. A high index of suspicion is needed to avoid missing such an injury, which is not an uncommon occurrence especially with undisplaced fractures. We present an unusual case of an undisplaced talar neck fracture in a five-year-old child leading to a delayed presentation of a symptomatic osteochondral loose body in the ankle joint. To our knowledge there are no reports in the literature of osteochondral loose bodies occurring in conjunction with an associated undisplaced talar neck fracture in either children or adults. The loose body was removed using anterior ankle arthroscopy. The child had an uneventful post operative recovery and regained full range of movement and function of his ankle joint and was discharged at one year follow-up. We aim to highlight the need to have a low threshold to further evaluate symptomatic children after fracture healing of an undisplaced talar neck fracture for a possible associated loose body in the ankle joint.
PMCID: PMC4095036  PMID: 25035846
Talus; Fracture; Loose body; Ankle arthroscopy; Children
6.  Patient Identified Disease Burden in Facioscapulohumeral Muscular Dystrophy 
Muscle & nerve  2012;46(6):951-953.
The multitude of symptoms associated with facioscapulohumeral muscular dystrophy (FSHD) disease burden are of varying importance. The extent of these symptoms and their cumulative effect on the FSHD population is unknown.
We conducted interviews with adult FSHD patients to identify which symptoms have the greatest effect on their lives. Each interview was recorded, transcribed, coded, and analyzed using a qualitative framework technique, triangulation, and 3-investigator consensus approach.
1375 quotes were obtained through 20 patient interviews. 251 symptoms of importance were identified representing 14 themes of FSHD disease burden. Symptoms associated with mobility impairment, activity limitation, and social role limitation were most frequently mentioned by participants.
There are multiple themes and symptoms, some previously under-recognized, that play a key role in FSHD disease burden.
PMCID: PMC4097080  PMID: 23225386
Facioscapulohumeral muscular dystrophy; quality of life; disease burden; neuromuscular disorders; symptoms
7.  Teaching Video NeuroImages: Trapezius myotonia percussion sign in myotonic dystrophy type 2 
Neurology  2013;80(24):e251.
Myotonic dystrophy type 2 (DM2) is an autosomal dominant disorder with proximal weakness, muscle pain, and early-onset cataracts.1 In comparison with myotonic dystrophy type 1 (DM1), myotonia is less symptomatic, more proximal, and harder to detect during clinical and electrodiagnostic testing.2 Here we document the presence of trapezius myotonia in patients with DM2 (video on the Neurology® Web site at In our experience, similar proximal percussion does not produce as marked a response in DM1 or nondystrophic myotonic disorders. This sign demonstrates a mechanism to test for proximal myotonia, and in at-risk patients, may be suggestive of an underlying diagnosis of DM2.
PMCID: PMC3721102  PMID: 23751923
8.  Enhanced Passive Bat Rabies Surveillance in Indigenous Bat Species from Germany - A Retrospective Study 
In Germany, rabies in bats is a notifiable zoonotic disease, which is caused by European bat lyssaviruses type 1 and 2 (EBLV-1 and 2), and the recently discovered new lyssavirus species Bokeloh bat lyssavirus (BBLV). As the understanding of bat rabies in insectivorous bat species is limited, in addition to routine bat rabies diagnosis, an enhanced passive surveillance study, i.e. the retrospective investigation of dead bats that had not been tested for rabies, was initiated in 1998 to study the distribution, abundance and epidemiology of lyssavirus infections in bats from Germany. A total number of 5478 individuals representing 21 bat species within two families were included in this study. The Noctule bat (Nyctalus noctula) and the Common pipistrelle (Pipistrellus pipistrellus) represented the most specimens submitted. Of all investigated bats, 1.17% tested positive for lyssaviruses using the fluorescent antibody test (FAT). The vast majority of positive cases was identified as EBLV-1, predominately associated with the Serotine bat (Eptesicus serotinus). However, rabies cases in other species, i.e. Nathusius' pipistrelle bat (Pipistrellus nathusii), P. pipistrellus and Brown long-eared bat (Plecotus auritus) were also characterized as EBLV-1. In contrast, EBLV-2 was isolated from three Daubenton's bats (Myotis daubentonii). These three cases contribute significantly to the understanding of EBLV-2 infections in Germany as only one case had been reported prior to this study. This enhanced passive surveillance indicated that besides known reservoir species, further bat species are affected by lyssavirus infections. Given the increasing diversity of lyssaviruses and bats as reservoir host species worldwide, lyssavirus positive specimens, i.e. both bat and virus need to be confirmed by molecular techniques.
Author Summary
According to the World Health Organization rabies is considered both a neglected zoonotic and a tropical disease. The causative agents are lyssaviruses which have their primary reservoir in bats. Although bat rabies is notifiable in Germany, the number of submitted bats during routine surveillance is rarely representative of the natural bat population. Therefore, the aim of this study was to include dead bats from various sources for enhanced bat rabies surveillance. The results show that a considerable number of additional bat rabies cases can be detected, thus improving the knowledge on the frequency, geographical distribution and reservoir-association of bat lyssavirus infections in Germany. The overall proportion of positives was lower than during routine surveillance in Germany. While the majority of cases were found in the Serotine bat and characterized as European bat lyssavirus type 1 (EBLV-1), three of the four EBLV-2 infections detected in Germany were found in Myotis daubentonii during this study.
PMCID: PMC4006713  PMID: 24784117
9.  Vampire Bat Rabies: Ecology, Epidemiology and Control 
Viruses  2014;6(5):1911-1928.
Extensive surveillance in bat populations in response to recent emerging diseases has revealed that this group of mammals acts as a reservoir for a large range of viruses. However, the oldest known association between a zoonotic virus and a bat is that between rabies virus and the vampire bat. Vampire bats are only found in Latin America and their unique method of obtaining nutrition, blood-feeding or haematophagy, has only evolved in the New World. The adaptations that enable blood-feeding also make the vampire bat highly effective at transmitting rabies virus. Whether the virus was present in pre-Columbian America or was introduced is much disputed, however, the introduction of Old World livestock and associated landscape modification, which continues to the present day, has enabled vampire bat populations to increase. This in turn has provided the conditions for rabies re-emergence to threaten both livestock and human populations as vampire bats target large mammals. This review considers the ecology of the vampire bat that make it such an efficient vector for rabies, the current status of vampire-transmitted rabies and the future prospects for spread by this virus and its control.
PMCID: PMC4036541  PMID: 24784570
vampire bat; Desmodus rotundus; rabies virus; transmission
10.  A Review of Emergency Cardiopulmonary Bypass for Severe Poisoning by Cardiotoxic Drugs 
Journal of Medical Toxicology  2012;9(1):54-60.
Cardiovascular collapse remains a leading cause of death in severe acute drug intoxication. Commonly prescribed medications such as antidysrhythmics, calcium channel antagonists, and beta adrenergic receptor antagonists can cause refractory cardiovascular collapse in massive overdose. Emergency cardiopulmonary bypass (ECPB), a modality originating in cardiac surgery, is a rescue technique that has been successfully implemented in the treatment of refractory cardiogenic shock and cardiac arrest unresponsive to traditional medical interventions. More recently a growing number of animal studies, case reports, and case series have documented its use in refractory hemodynamic collapse in poisoned patients. This article will review current ECPB techniques and explore its growing role in the treatment of severely hemodynamically compromised poisoned patients.
PMCID: PMC3576497  PMID: 23238774
Emergency cardiopulmonary bypass; Extracorporeal membrane oxygenation; Extracorporeal life support; Cardiogenic shock; Cardiotoxic drugs
11.  Comparative neuronal morphology of the cerebellar cortex in afrotherians, carnivores, cetartiodactyls, and primates 
Although the basic morphological characteristics of neurons in the cerebellar cortex have been documented in several species, virtually nothing is known about the quantitative morphological characteristics of these neurons across different taxa. To that end, the present study investigated cerebellar neuronal morphology among eight different, large-brained mammalian species comprising a broad phylogenetic range: afrotherians (African elephant, Florida manatee), carnivores (Siberian tiger, clouded leopard), cetartiodactyls (humpback whale, giraffe) and primates (human, common chimpanzee). Specifically, several neuron types (e.g., stellate, basket, Lugaro, Golgi, and granule neurons; N = 317) of the cerebellar cortex were stained with a modified rapid Golgi technique and quantified on a computer-assisted microscopy system. There was a 64-fold variation in brain mass across species in our sample (from clouded leopard to the elephant) and a 103-fold variation in cerebellar volume. Most dendritic measures tended to increase with cerebellar volume. The cerebellar cortex in these species exhibited the trilaminate pattern common to all mammals. Morphologically, neuron types in the cerebellar cortex were generally consistent with those described in primates (Fox et al., 1967) and rodents (Palay and Chan-Palay, 1974), although there was substantial quantitative variation across species. In particular, Lugaro neurons in the elephant appeared to be disproportionately larger than those in other species. To explore potential quantitative differences in dendritic measures across species, MARSplines analyses were used to evaluate whether species could be differentiated from each other based on dendritic characteristics alone. Results of these analyses indicated that there were significant differences among all species in dendritic measures.
PMCID: PMC4005950  PMID: 24795574
dendrite; morphometry; Golgi method; brain evolution; cerebellum
13.  Simple mathematical law benchmarks human confrontations 
Scientific Reports  2013;3:3463.
Many high-profile societal problems involve an individual or group repeatedly attacking another – from child-parent disputes, sexual violence against women, civil unrest, violent conflicts and acts of terror, to current cyber-attacks on national infrastructure and ultrafast cyber-trades attacking stockholders. There is an urgent need to quantify the likely severity and timing of such future acts, shed light on likely perpetrators, and identify intervention strategies. Here we present a combined analysis of multiple datasets across all these domains which account for >100,000 events, and show that a simple mathematical law can benchmark them all. We derive this benchmark and interpret it, using a minimal mechanistic model grounded by state-of-the-art fieldwork. Our findings provide quantitative predictions concerning future attacks; a tool to help detect common perpetrators and abnormal behaviors; insight into the trajectory of a ‘lone wolf'; identification of a critical threshold for spreading a message or idea among perpetrators; an intervention strategy to erode the most lethal clusters; and more broadly, a quantitative starting point for cross-disciplinary theorizing about human aggression at the individual and group level, in both real and online worlds.
PMCID: PMC3857569  PMID: 24322528
14.  A Survey of Rural Hospitals’ Perspectives on Health Information Technology Outsourcing 
A survey of rural hospitals was conducted in the spring of 2012 to better understand their perspectives on health information technology (HIT) outsourcing and the role that hospital-to-hospital HIT partnerships (HHPs) can play as an outsourcing mechanism. The survey sought to understand how HHPs might be leveraged for HIT implementation, as well as the challenges with forming them. The results suggest that HHPs have the potential to address rural hospitals’ slow rate of HIT adoption, but there are also challenges to creating these partnerships. These issues, as well as avenues for further research, are then discussed.
PMCID: PMC3900214  PMID: 24551373
15.  The Signal Sequence Influences Post-Translational ER Translocation at Distinct Stages 
PLoS ONE  2013;8(10):e75394.
The metazoan Sec61 translocon transports polypeptides into and across the membrane of the endoplasmic reticulum via two major routes, a well-established co-translational pathway and a post-translational alternative. We have used two model substrates to explore the elements of a secretory protein precursor that preferentially direct it towards a co- or post-translational pathway for ER translocation. Having first determined the capacity of precursors to enter ER derived microsomes post-translationally, we then exploited semi-permeabilized mammalian cells specifically depleted of key membrane components using siRNA to address their contribution to the membrane translocation process. These studies suggest precursor chain length is a key factor in the post-translational translocation at the mammalian ER, and identify Sec62 and Sec63 as important components acting on this route. This role for Sec62 and Sec63 is independent of the signal sequence that delivers the precursor to the ER. However, the signal sequence can influence the subsequent membrane translocation process, conferring sensitivity to a small molecule inhibitor and dictating reliance on the molecular chaperone BiP. Our data support a model where secretory protein precursors that fail to engage the signal recognition particle, for example because they are short, are delivered to the ER membrane via a distinct route that is dependent upon both Sec62 and Sec63. Although this requirement for Sec62 and Sec63 is unaffected by the specific signal sequence that delivers a precursor to the ER, this region can influence subsequent events, including both Sec61 mediated transport and the importance of BiP for membrane translocation. Taken together, our data suggest that an ER signal sequence can regulate specific aspects of Sec61 mediated membrane translocation at a stage following Sec62/Sec63 dependent ER delivery.
PMCID: PMC3793985  PMID: 24130708
16.  European Surveillance for West Nile Virus in Mosquito Populations 
A wide range of arthropod-borne viruses threaten both human and animal health either through their presence in Europe or through risk of introduction. Prominent among these is West Nile virus (WNV), primarily an avian virus, which has caused multiple outbreaks associated with human and equine mortality. Endemic outbreaks of West Nile fever have been reported in Italy, Greece, France, Romania, Hungary, Russia and Spain, with further spread expected. Most outbreaks in Western Europe have been due to infection with WNV Lineage 1. In Eastern Europe WNV Lineage 2 has been responsible for human and bird mortality, particularly in Greece, which has experienced extensive outbreaks over three consecutive years. Italy has experienced co-circulation with both virus lineages. The ability to manage this threat in a cost-effective way is dependent on early detection. Targeted surveillance for pathogens within mosquito populations offers the ability to detect viruses prior to their emergence in livestock, equine species or human populations. In addition, it can establish a baseline of mosquito-borne virus activity and allow monitoring of change to this over time. Early detection offers the opportunity to raise disease awareness, initiate vector control and preventative vaccination, now available for horses, and encourage personal protection against mosquito bites. This would have major benefits through financial savings and reduction in equid morbidity/mortality. However, effective surveillance that predicts virus outbreaks is challenged by a range of factors including limited resources, variation in mosquito capture rates (too few or too many), difficulties in mosquito identification, often reliant on specialist entomologists, and the sensitive, rapid detection of viruses in mosquito pools. Surveillance for WNV and other arboviruses within mosquito populations varies between European countries in the extent and focus of the surveillance. This study reviews the current status of WNV in mosquito populations across Europe and how this is informing our understanding of virus epidemiology. Key findings such as detection of virus, presence of vector species and invasive mosquito species are summarized, and some of the difficulties encountered when applying a cost-effective surveillance programme are highlighted.
PMCID: PMC3823308  PMID: 24157510
West Nile virus; mosquito; surveillance; vector; invasive species
17.  Global Epigenomic Reconfiguration During Mammalian Brain Development 
Science (New York, N.Y.)  2013;341(6146):1237905.
DNA methylation is implicated in mammalian brain development and plasticity underlying learning and memory. We report the genome-wide composition, patterning, cell specificity, and dynamics of DNA methylation at single-base resolution in human and mouse frontal cortex throughout their lifespan. Widespread methylome reconfiguration occurs during fetal to young adult development, coincident with synaptogenesis. During this period, highly conserved non-CG methylation (mCH) accumulates in neurons, but not glia, to become the dominant form of methylation in the human neuronal genome. Moreover, we found an mCH signature that identifies genes escaping X-chromosome inactivation. Last, whole-genome single-base resolution 5-hydroxymethylcytosine (hmC) maps revealed that hmC marks fetal brain cell genomes at putative regulatory regions that are CG-demethylated and activated in the adult brain and that CG demethylation at these hmC-poised loci depends on Tet2 activity.
PMCID: PMC3785061  PMID: 23828890
18.  Abrupt rise of new machine ecology beyond human response time 
Scientific Reports  2013;3:2627.
Society's techno-social systems are becoming ever faster and more computer-orientated. However, far from simply generating faster versions of existing behaviour, we show that this speed-up can generate a new behavioural regime as humans lose the ability to intervene in real time. Analyzing millisecond-scale data for the world's largest and most powerful techno-social system, the global financial market, we uncover an abrupt transition to a new all-machine phase characterized by large numbers of subsecond extreme events. The proliferation of these subsecond events shows an intriguing correlation with the onset of the system-wide financial collapse in 2008. Our findings are consistent with an emerging ecology of competitive machines featuring ‘crowds' of predatory algorithms, and highlight the need for a new scientific theory of subsecond financial phenomena.
PMCID: PMC3769652  PMID: 24022120
19.  Patient-reported impact of symptoms in myotonic dystrophy type 1 (PRISM-1) 
Neurology  2012;79(4):348-357.
To determine the most critical symptoms in a national myotonic dystrophy type 1 (DM1) population and to identify the modifying factors that have the greatest effect on the severity of these symptoms.
We performed a cross-sectional study of 278 adult patients with DM1 from the national registry of patients with DM1 between April and August 2010. We assessed the prevalence and relative significance of 221 critical DM1 symptoms and 14 disease themes. These symptoms and themes were chosen for evaluation based on prior interviews with patients with DM1. Responses were categorized by age, CTG repeat length, gender, and duration of symptoms.
Participants with DM1 provided symptom rating survey responses to address the relative frequency and importance of each DM1 symptom. The symptomatic themes with the highest prevalence in DM1 were problems with hands or arms (93.5%), fatigue (90.8%), myotonia (90.3%), and impaired sleep or daytime sleepiness (87.9%). Participants identified fatigue and limitations in mobility as the symptomatic themes that have the greatest effect on their lives. We found an association between age and the average prevalence of all themes (p < 0.01) and between CTG repeat length and the average effect of all symptomatic themes on participant lives (p < 0.01).
There are a wide range of symptoms that significantly affect the lives of patients with DM1. These symptoms, some previously underrecognized, have varying levels of importance in the DM1 population and are nonlinearly dependent on patient age and CTG repeat length.
PMCID: PMC3400095  PMID: 22786587
20.  Louping Ill Virus Genome Sequence Derived from the Spinal Cord of an Infected Lamb 
Genome Announcements  2013;1(4):e00454-13.
Louping ill virus (LIV) is a zoonotic virus causing fatal encephalitis in young sheep and grouse. We have recovered the complete genome sequence from a spinal cord sample prepared from a lamb that was naturally infected with LIV. This is only the second LIV genome sequence reported and the first prepared from a clinical sample.
PMCID: PMC3715664  PMID: 23868122
21.  The cell morphogenesis ANGUSTIFOLIA (AN) gene, a plant homolog of CtBP/BARS, is involved in abiotic and biotic stress response in higher plants 
BMC Plant Biology  2013;13:79.
ANGUSTIFOLIA (AN), one of the CtBP family proteins, plays a major role in microtubule-dependent cell morphogenesis. Microarray analysis of mammalian AN homologs suggests that AN might function as a transcriptional activator and regulator of a wide range of genes. Genetic characterization of AN mutants suggests that AN might be involved in multiple biological processes beyond cell morphology regulation.
Using a reverse genetic approach, we provide in this paper the genetic, biochemical, and physiological evidence for ANGUSTIFOLIA’s role in other new biological functions such as abiotic and biotic stress response in higher plants. The T-DNA knockout an-t1 mutant exhibits not only all the phenotypes of previously described angustifolia null mutants, but also copes better than wild type under dehydration and pathogen attack. The stress tolerance is accompanied by a steady-state modulation of cellular H2O2 content, malondialdehyde (MDA) derived from cellular lipid peroxidation, and over-expression of stress responsive genes. Our results indicate that ANGUSTIFOLIA functions beyond cell morphology control through direct or indirect functional protein interaction networks mediating other biological processes such as drought and pathogen attacks.
Our results indicate that the ANGUSTIFOLIA gene participates in several biochemical pathways controlling cell morphogenesis, abiotic, and biotic stress responses in higher plants. Our results suggest that the in vivo function of plant ANGUSTIFOLIA has been overlooked and it needs to be further studied beyond microtubule-dependent cell morphogenesis.
PMCID: PMC3663690  PMID: 23672620
Angustifolia; Cell morphogenesis; Arabidopsis thaliana; Abiotic stress; Biotic stress; T-DNA knockout mutant
22.  Genetic Architecture of Skin and Eye Color in an African-European Admixed Population 
PLoS Genetics  2013;9(3):e1003372.
Variation in human skin and eye color is substantial and especially apparent in admixed populations, yet the underlying genetic architecture is poorly understood because most genome-wide studies are based on individuals of European ancestry. We study pigmentary variation in 699 individuals from Cape Verde, where extensive West African/European admixture has given rise to a broad range in trait values and genomic ancestry proportions. We develop and apply a new approach for measuring eye color, and identify two major loci (HERC2[OCA2] P = 2.3×10−62, SLC24A5 P = 9.6×10−9) that account for both blue versus brown eye color and varying intensities of brown eye color. We identify four major loci (SLC24A5 P = 5.4×10−27, TYR P = 1.1×10−9, APBA2[OCA2] P = 1.5×10−8, SLC45A2 P = 6×10−9) for skin color that together account for 35% of the total variance, but the genetic component with the largest effect (∼44%) is average genomic ancestry. Our results suggest that adjacent cis-acting regulatory loci for OCA2 explain the relationship between skin and eye color, and point to an underlying genetic architecture in which several genes of moderate effect act together with many genes of small effect to explain ∼70% of the estimated heritability.
Author Summary
Differences in skin and eye color are some of the most obvious traits that underlie human diversity, yet most of our knowledge regarding the genetic basis for these traits is based on the limited range of variation represented by individuals of European ancestry. We have studied a unique population in Cape Verde, an archipelago located off the West African coast, in which extensive mixing between individuals of Portuguese and West African ancestry has given rise to a broad range of phenotypes and ancestral genome proportions. Our results help to explain how genes work together to control the full range of pigmentary phenotypic diversity, provide new insight into the evolution of these traits, and provide a model for understanding other types of quantitative variation in admixed populations.
PMCID: PMC3605137  PMID: 23555287
23.  A Role for the Malignant Brain Tumour (MBT) Domain Protein LIN-61 in DNA Double-Strand Break Repair by Homologous Recombination 
PLoS Genetics  2013;9(3):e1003339.
Malignant brain tumour (MBT) domain proteins are transcriptional repressors that function within Polycomb complexes. Some MBT genes are tumour suppressors, but how they prevent tumourigenesis is unknown. The Caenorhabditis elegans MBT protein LIN-61 is a member of the synMuvB chromatin-remodelling proteins that control vulval development. Here we report a new role for LIN-61: it protects the genome by promoting homologous recombination (HR) for the repair of DNA double-strand breaks (DSBs). lin-61 mutants manifest numerous problems associated with defective HR in germ and somatic cells but remain proficient in meiotic recombination. They are hypersensitive to ionizing radiation and interstrand crosslinks but not UV light. Using a novel reporter system that monitors repair of a defined DSB in C. elegans somatic cells, we show that LIN-61 contributes to HR. The involvement of this MBT protein in HR raises the possibility that MBT–deficient tumours may also have defective DSB repair.
Author Summary
The genome is continually under threat from exogenous sources of DNA damage, as well as from sources that originate within the cell. DNA double-strand breaks (DSBs) are arguably the most problematic type of damage as they can cause dangerous chromosome rearrangements, which can lead to cancer, as well as mutation at the break site and/or cell death. A complex network of molecular pathways, collectively referred to as the DNA damage response (DDR), have evolved to protect the cell from these threats. We have discovered a new DDR factor, LIN-61, that promotes the repair of DSBs. This is a novel and unexpected role for LIN-61, which was previously known to act as a regulator of gene transcription during development.
PMCID: PMC3591299  PMID: 23505385
24.  COM-1 Promotes Homologous Recombination during Caenorhabditis elegans Meiosis by Antagonizing Ku-Mediated Non-Homologous End Joining 
PLoS Genetics  2013;9(2):e1003276.
Successful completion of meiosis requires the induction and faithful repair of DNA double-strand breaks (DSBs). DSBs can be repaired via homologous recombination (HR) or non-homologous end joining (NHEJ), yet only repair via HR can generate the interhomolog crossovers (COs) needed for meiotic chromosome segregation. Here we identify COM-1, the homolog of CtIP/Sae2/Ctp1, as a crucial regulator of DSB repair pathway choice during Caenorhabditis elegans gametogenesis. COM-1–deficient germ cells repair meiotic DSBs via the error-prone pathway NHEJ, resulting in a lack of COs, extensive chromosomal aggregation, and near-complete embryonic lethality. In contrast to its yeast counterparts, COM-1 is not required for Spo11 removal and initiation of meiotic DSB repair, but instead promotes meiotic recombination by counteracting the NHEJ complex Ku. In fact, animals defective for both COM-1 and Ku are viable and proficient in CO formation. Further genetic dissection revealed that COM-1 acts parallel to the nuclease EXO-1 to promote interhomolog HR at early pachytene stage of meiotic prophase and thereby safeguards timely CO formation. Both of these nucleases, however, are dispensable for RAD-51 recruitment at late pachytene stage, when homolog-independent repair pathways predominate, suggesting further redundancy and/or temporal regulation of DNA end resection during meiotic prophase. Collectively, our results uncover the potentially lethal properties of NHEJ during meiosis and identify a critical role for COM-1 in NHEJ inhibition and CO assurance in germ cells.
Author Summary
Sexually reproducing animals create germ cells via meiosis, a cell division program that requires the induction and faithful repair of DNA double-strand breaks (DSBs). Meiotic DSBs are typically repaired via homologous recombination (HR), an error-free repair pathway that generates transient links between homologous chromosomes, named crossovers (COs), which are needed for proper chromosome segregation. To date, it is unclear how germ cells channel these programmed DSBs into HR and not into error-prone DSB repair pathways such as non-homologous end joining (NHEJ). We used the genetically tractable animal model Caenorhabditis elegans to study the mechanisms underlying the strong HR bias in germ cells. Here, we identify COM-1, the worm homolog of CtIP, as a crucial regulator of meiotic DSB repair pathway choice: COM-1 effectively blocks the action of the NHEJ complex Ku, thereby assuring correct repair via HR. In addition, we show that unscheduled NHEJ activity during meiosis leads to a lack of COs, extensive chromosomal aggregation, and near-complete embryonic lethality. Further genetic dissection also revealed a redundant and stage-specific role for COM-1 in meiotic HR. Our work thus establishes COM-1/CtIP as a caretaker of germline genome stability and unveils meiotic NHEJ as a potent source of chromosomal aberrations in newborns.
PMCID: PMC3567172  PMID: 23408909
25.  Genome-wide association study of body height in African Americans: the Women's Health Initiative SNP Health Association Resource (SHARe) 
Human Molecular Genetics  2011;21(3):711-720.
Height is a complex trait under strong genetic influence. To date, numerous genetic loci have been associated with height in individuals of European ancestry. However, few large-scale discovery genome-wide association studies (GWAS) of height in minority populations have been conducted and thus information about population-specific height regulation is limited. We conducted a GWA analysis of height in 8149 African-American (AA) women from the Women's Health Initiative. Genetic variants with P< 5 × 10−5 (n = 169) were followed up in a replication data set (n = 20 809) and meta-analyzed in a total of 28 958 AAs and African-descent individuals. Twelve single-nucleotide polymorphisms (SNPs) representing 7 independent loci were significantly associated with height at P < 5 × 10−8. We identified novel SNPs in 17q23 (TMEM100/PCTP) and Xp22.3 (ARSE) reflecting population-specific regulation of height in AAs and replicated five loci previously reported in European-descent populations [4p15/LCORL, 11q13/SERPINH1, 12q14/HMGA2, 17q23/MAP3K3 (mitogen-activated protein kinase3) and 18q21/DYM]. In addition, we performed an admixture mapping analysis of height which is both complementary and supportive to the GWA analysis and suggests potential associations between ancestry and height on chromosomes 4 (4q21), 15 (15q26) and 17 (17q23). Our findings provide insight into the genetic architecture of height and support the investigation of non-European-descent populations for identifying genetic factors associated with complex traits. Specifically, we identify new loci that may reflect population-specific regulation of height and report several known height loci that are important in determining height in African-descent populations.
PMCID: PMC3259012  PMID: 22021425

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