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PubMed | Epidemiology and. and Genetics.
Type: Journal Article | Journal: Annual review of virology | Year: 2016

Coronaviruses have frequently expanded their host range in recent history, with two events resulting in severe disease outbreaks in human populations. Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2003 in Southeast Asia and rapidly spread around the world before it was controlled by public health intervention strategies. The 2012 Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak represents another prime example of virus emergence from a zoonotic reservoir. Here, we review the current knowledge of coronavirus cross-species transmission, with particular focus on MERS-CoV. MERS-CoV is still circulating in the human population, and the mechanisms governing its cross-species transmission have been only partially elucidated, highlighting a need for further investigation. We discuss biochemical determinants mediating MERS-CoV host cell permissivity, including virus spike interactions with the MERS-CoV cell surface receptor dipeptidyl peptidase 4 (DPP4), and evolutionary mechanisms that may facilitate host range expansion, including recombination, mutator alleles, and mutational robustness. Understanding these mechanisms can help us better recognize the threat of emergence for currently circulating zoonotic strains.


Dadd T.,Colworth Science Park | Lewis C.M.,Genetics | Lewis C.M.,King's College London | Weale M.E.,Genetics
Human Heredity | Year: 2010

Objective: To investigate the validity of simulations and assumptions used to underpin the delta-centralization (DC) method for correcting for population stratification in genetic association studies; to assess the effectiveness of DC compared to genomic control (GC) under valid simulation conditions; and to highlight other studies employing similarly flawed simulations. Methods: DC and GC use data from unlinked null loci to correct the test statistic at the target locus, but differ in the way the correction is performed. We compare DC and GC under two simulation approaches: an invalid approach adopted by the originators of DC, which permits subpopulation allele frequency matching of null markers to the target locus; and a valid approach, based on the Balding-Nichols model, which does not allow subpopulation matching. Results: DC works under invalid simulation conditions (subpopulation allele frequency matching), but not under our valid ones. We use theoretical arguments to assert that there are no valid conditions under which DC might work. We identify several studies which have adopted similarly invalid simulation approaches in this field. Conclusion: DC fails to control for population stratification and should not be used. Other results from studies which have used the same invalid simulation approach should be treated cautiously. © 2010 S. Karger AG, Basel.


Williams F.M.,King's College London | MOnica Risk,Genetics
Annals of neurology | Year: 2013

End-stage coagulation and the structure/function of fibrin are implicated in the pathogenesis of ischemic stroke. We explored whether genetic variants associated with end-stage coagulation in healthy volunteers account for the genetic predisposition to ischemic stroke and examined their influence on stroke subtype. Common genetic variants identified through genome-wide association studies of coagulation factors and fibrin structure/function in healthy twins (n = 2,100, Stage 1) were examined in ischemic stroke (n = 4,200 cases) using 2 independent samples of European ancestry (Stage 2). A third clinical collection having stroke subtyping (total 8,900 cases, 55,000 controls) was used for replication (Stage 3). Stage 1 identified 524 single nucleotide polymorphisms (SNPs) from 23 linkage disequilibrium blocks having significant association (p < 5 × 10(-8)) with 1 or more coagulation/fibrin phenotypes. The most striking associations included SNP rs5985 with factor XIII activity (p = 2.6 × 10(-186)), rs10665 with FVII (p = 2.4 × 10(-47)), and rs505922 in the ABO gene with both von Willebrand factor (p = 4.7 × 10(-57)) and factor VIII (p = 1.2 × 10(-36)). In Stage 2, the 23 independent SNPs were examined in stroke cases/noncases using MOnica Risk, Genetics, Archiving and Monograph (MORGAM) and Wellcome Trust Case Control Consortium 2 collections. SNP rs505922 was nominally associated with ischemic stroke (odds ratio = 0.94, 95% confidence interval = 0.88-0.99, p = 0.023). Independent replication in Meta-Stroke confirmed the rs505922 association with stroke, beta (standard error, SE) = 0.066 (0.02), p = 0.001, a finding specific to large-vessel and cardioembolic stroke (p = 0.001 and p = < 0.001, respectively) but not seen with small-vessel stroke (p = 0.811). ABO gene variants are associated with large-vessel and cardioembolic stroke but not small-vessel disease. This work sheds light on the different pathogenic mechanisms underpinning stroke subtype. Copyright © 2012 American Neurological Association.


Evans M.I.,Columbia University | Wright D.A.,University of Plymouth | Pergament E.,Genetics | Cuckle H.S.,Columbia University | Nicolaides K.H.,Foundation Medicine
Fetal Diagnosis and Therapy | Year: 2012

Objective: To determine the feasibility of digital PCR analysis for noninvasive prenatal diagnosis of trisomy 21. Methods: Through power equations, we modeled the number of wells necessary to determine the feasibility of digital PCR as a practical method for trisomy 21 risk assessment. Results: The number of wells needed is a direct correlate of the ability to isolate free fetal DNA. If a 20% fetal DNA enhancement can be achieved, then 2,609 counts would be sufficient to achieve a 99% detection rate for a 1% false-positive rate and potentially feasible with readily available plates. However, if only a 2% increase is seen, then 220,816 counts will be necessary, and over 110,000 would be needed just to achieve 95% for a 5% false-positive rate - both far beyond current commercially available technology. Conclusion: There are several noninvasive prenatal diagnostic methods which may reach commercialization; all have differing potential advantages and disadvantages. Digital PCR is potentially a cheaper methodology for trisomy 21, but it is too early to determine the optimal method. Copyright © 2012 S. Karger AG.


Wang H.,Genetics | Wang H.,Zhejiang University | Liu K.,Zhejiang University | Geng M.,Genetics | And 9 more authors.
Cancer Research | Year: 2013

The transcription factor NRF2 (NFE2L2) is a pivotal activator of genes encoding cytoprotective and detoxifying enzymes that limit the action of cytotoxic therapies in cancer. NRF2 acts by binding antioxidant response elements (ARE) in its target genes, but there is relatively limited knowledge about how it is negatively controlled. Here, we report that retinoic X receptor alpha (RXRalpha;) is a hitherto unrecognized repressor of NRF2. RNAi-mediated knockdown of RXRa increased basal ARE-driven gene expression and induction of ARE-driven genes by the NRF2 activator tert-butylhydroquinone (tBHQ). Conversely, overexpression of RXRa decreased ARE-driven gene expression. Biochemical investigations showed that RXRa interacts physically with NRF2 in cancer cells and in murine small intestine and liver tissues. Furthermore, RXRa bound to ARE sequences in the promoters of NRF2-regulated genes. RXRa loading onto AREs was concomitant with the presence of NRF2, supporting the hypothesis that a direct interaction between the two proteins on gene promoters accounts for the antagonism of ARE-driven gene expression. Mutation analyses revealed that interaction between the two transcription factors involves the DNA-binding domain of RXRa and a region comprising amino acids 209-316 in human NRF2 that had not been defined functionally, but that we now designate as the NRF2-ECH homology (Neh) 7 domain. In non-small cell lung cancer cells where NRF2 levels are elevated, RXRa expression downregulated NRF2 and sensitized cells to the cytotoxic effects of therapeutic drugs. In summary, our findings show that RXRa diminishes cytoprotection by NRF2 by binding directly to the newly defined Neh7 domain in NRF2. Cancer Res; 73(10); 3097-108. © 2013 AACR.


Velasco P.,Genetics | Lema M.,University of Santiago de Compostela | Francisco M.,Genetics | Soengas P.,Genetics | Elena Cartea M.,Genetics
Molecules | Year: 2013

Brassica rapa is a crucifer that is grown worldwide, mainly as a vegetable. The quality of B. rapa crops is highly affected by the disease caused by the bacteria Xanthomonas campestris pv. campestris (Xcc). Glucosinolates and phenolic compounds can confer resistance to Brassica crops against pests and diseases, but few works have been done to evaluate their role in Xcc resistance. The objectives of this work were: (1) to evaluate the in vivo and in vitro antibacterial effect of gluconapin, its isothiocyanate and the methanolic extracts of B. rapa against the type 4 of Xcc, and (2) to test if there is induced resistance mediated by glucosinolates or phenolic compounds in two varieties of B. rapa. Gluconapin and its ITC varieties had an antibacterial effect on the development of Xanthomonas and this effect was strongly dependent on the concentration applied. Methanolic extracts from B. rapa, containing glucosinolates and phenolic compounds, inhibited the growth of these bacteria. Concentration of gluconapin is higher in resistant plants than in the susceptible ones and there is an induction of gluconapin, some flavonoids and sinapic acid 48 to 72 h after inoculation. Gluconapin plays a role in the constitutive resistance to Xcc, while gluconapin, some flavonoids and hydroxycinnamic acids are induced by a Xcc infection but it is not clear if this induction confers resistance to this disease. © 2013 by the authors.


Al-Bulushi B.,Prince Sultan Military Medical City | Al-Hashem A.,Genetics | Tabarki B.,Prince Sultan Military Medical City
Journal of Child Neurology | Year: 2014

The clinical spectrum associated with ATP1A2 mutations is expanding and includes familial hemiplegic migraine, alternating hemiplegia of childhood, and epilepsy. We have identified a novel c.1766T>C. (Ile589Thr) heterozygous mutation in the ATP1A2 gene in a Saudi kindred with hemiplegic attacks and seizures. Our findings broaden the phenotypic spectrum of patients with ATP1A2 mutations. © The Author(s) 2013.


Riisgard H.U.,University of Southern Denmark | Funch P.,Genetics | Larsen P.S.,Technical University of Denmark
Acta Zoologica | Year: 2015

Filter feeding in mussels is a secondary adaptation where the gills have become W-shaped and greatly enlarged, acting as the mussel filter-pump. Water pumping and particle capture in the blue mussel, Mytilus edulis, have been studied over many years. Here, we give a short status of the present understanding of ciliary structure and function of the mussel filter-pump, supplemented with new photo-microscope and scanning electron microscopy (SEM) pictures of gill preparations. Pumping rate (filtration) and pressure to maintain flow have been extensively studied so the power delivered by the mussel pump to the water flow is known (1.1% of total respiratory power), but the actual cost based on gill respiration is much higher (19%), implying that the cost of maintaining of the large gill pump is considerable and that only relatively little energy can be saved by stopping or reducing the activity of the water-pumping cilia so that continuous feeding with a 'minimal scaled' pump is cheaper than discontinuous feeding with a correspondingly larger pump. According to the present view, the pump proper is the beating lateral cilia (lc) on the gill filaments and particle capture is accomplished by the action of laterofrontal cirri (lfc) transferring particles from the main water current to the frontal gill filament currents driven by frontal cilia (fc). Unexplained aspects include retention efficiency according to particle size and the role of pro-laterofrontal cilia (p-lfc) placed between the lfc and fc. The structure of cilia and the mode of ciliary beating have been re-examined in this study by new high-resolution light and scanning electron microscopy of isolated gill preparations exposed to serotonin (5-HT) stimulation which can activate the lc and lfc at low concentrations (10-6 M), but removes the lfc from the interfilament canals at higher concentrations (10-5 M). © 2014 The Royal Swedish Academy of Sciences.


Hornyik C.,Genetics | Terzi L.C.,University of Dundee | Simpson G.G.,Genetics | Simpson G.G.,University of Dundee
Developmental Cell | Year: 2010

The spen family protein FPA is required for flowering time control and has been implicated in RNA silencing. The mechanism by which FPA carries out these functions is unknown. We report the identification of an activity for FPA in controlling mRNA 3′ end formation. We show that FPA functions redundantly with FCA, another RNA binding protein that controls flowering and RNA silencing, to control the expression of alternatively polyadenylated antisense RNAs at the locus encoding the floral repressor FLC. In addition, we show that defective 3′ end formation at an upstream RNA polymerase II-dependent gene explains the apparent derepression of the AtSN1 retroelement in fpa mutants. Transcript readthrough accounts for the absence of changes in DNA methylation and siRNA abundance at AtSN1 in fpa mutants, and this may explain other examples of epigenetic transitions not associated with chromatin modification. © 2010 Elsevier Inc. All rights reserved.


PubMed | Lady Hardinge Medical College and Genetics
Type: Journal Article | Journal: Journal of clinical ultrasound : JCU | Year: 2016

A fetus with skeletal disorder poses diagnostic challenges in a resource-poor setting with limited management options. The objective of the study was to develop a step-by-step approach for the diagnosis of skeletal dysplasia in light of the limited resources available.An algorithmic approach was used. The assessment for lethality was the first step, followed by the evaluation for fractures. In cases without evidence of fracture, severe constriction of thorax or associated polydactyly were searched for. In cases without severe thoracic constriction, the severity of micromelia was evaluated. After delivery, fetal examination was done to ascertain the etiology.During the 6-year period, 41 cases with shortened long bones were fully evaluated. Lethality was suspected in 30 cases. Fracture and beading were present in eight cases, and severe thoracic constriction with polydactyly was observed in seven cases. Mild micromelia was seen in 19 cases and severe micromelia in 7 cases. Among lethal skeletal dysplasias, thanatophoric dysplasia was most common (six cases). Among nonlethal skeletal dysplasias, achondroplasia was seen in eight cases.Lethality of skeletal dysplasia could be predicted on prenatal ultrasound with 100% accuracy. The step-by-step approach was helpful to characterize skeletal dysplasias. 2016 Wiley Periodicals, Inc. J Clin Ultrasound 44:529-539, 2016.

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