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1.  Frataxin-bypassing Isu1: characterization of the bypass activity in cells and mitochondria 
The Biochemical journal  2014;459(1):71-81.
Frataxin is a conserved mitochondrial protein, and deficiency underlies the neurodegenerative disease Friedreich’s ataxia. Frataxin interacts with the core machinery for Fe–S cluster assembly in mitochondria. Recently we reported that in frataxin-deleted yeast strains, a spontaneously occurring mutation in one of two genes encoding redundant Isu scaffold proteins, bypassed the mutant phenotypes. In the present study we created strains expressing a single scaffold protein, either Isu1 or the bypass mutant M107I Isu1. Our results show that in the frataxin-deletion strain expressing the bypass mutant Isu1, cell growth, Fe–S cluster protein activities, haem proteins and iron homoeostasis were restored to normal or close to normal. The bypass effects were not mediated by changes in Isu1 expression level. The persulfide-forming activity of the cysteine desulfurase was diminished in the frataxin deletion (Δyfh1 ISU1) and was improved by expression of the bypass Isu1 (Δyfh1 M107I ISU1). The addition of purified bypass M107I Isu1 protein to a Δyfh1 lysate conferred similar enhancement of cysteine desulfurase as did frataxin, suggesting that this effect contributed to the bypass mechanism. Fe–S cluster-forming activity in isolated mitochondria was stimulated by the bypass Isu1, albeit at a lower rate. The rescuing effects of the bypass Isu1 point to ways that the core defects in Friedreich’s ataxia mitochondria can be restored.
doi:10.1042/BJ20131273
PMCID: PMC4021491  PMID: 24433162
cysteine desulfurase; eukaryote; frataxin; iron–sulfur; Isu1 scaffold; mitochondrion
2.  Mutation in the Fe–S scaffold protein Isu bypasses frataxin deletion 
The Biochemical journal  2012;441(1):473-480.
Frataxin is a conserved mitochondrial protein deficient in patients with Friedreich’s ataxia. Frataxin has been implicated in control of iron homoeostasis and Fe–S cluster assembly. In yeast or human mitochondria, frataxin interacts with components of the Fe–S cluster synthesis machinery, including the cysteine desulfurase Nfs1, accessory protein Isd11 and scaffold protein Isu. In the present paper, we report that a single amino acid substitution (methionine to isoleucine) at position 107 in the mature form of Isu1 restored many deficient functions in Δyfh1 or frataxin-depleted yeast cells. Iron homoeostasis was improved such that soluble/usable mitochondrial iron was increased and accumulation of insoluble/non-usable iron within mitochondria was largely prevented. Cytochromes were returned to normal and haem synthesis was restored. In mitochondria carrying the mutant Isu1 and no frataxin, Fe–S cluster enzyme activities were improved. The efficiency of newFe–S cluster synthesis in isolated mitochondria was markedly increased compared with frataxin-negative cells, although the response to added iron was minimal. The M107I substitution in the highly conserved Isu scaffold protein is typically found in bacterial orthologues, suggesting that a unique feature of the bacterial Fe–S cluster machinery may be involved. The mechanism by which the mutant Isu bypasses the absence of frataxin remains to be determined, but could be related to direct effects on Fe–S cluster assembly and/or indirect effects on mitochondrial iron availability.
doi:10.1042/BJ20111637
PMCID: PMC4018837  PMID: 21936771
frataxin; haem; iron; iron–sulfur cluster (Fe–S cluster); mitochondrion
3.  Transcriptome analysis of chicken ES, blastodermal and germ cells reveals that chick ES cells are equivalent to mouse ES cells rather than EpiSC 
Stem Cell Research  2015;14(1):54-67.
Pluripotent Embryonic Stem cell (ESC) lines can be derived from a variety of sources. Mouse lines derived from the early blastocyst and from primordial germ cells (PGCs) can contribute to all somatic lineages and to the germ line, whereas cells from slightly later embryos (EpiSC) no longer contribute to the germ line. In chick, pluripotent ESCs can be obtained from PGCs and from early blastoderms. Established PGC lines and freshly isolated blastodermal cells (cBC) can contribute to both germinal and somatic lineages but established lines from the former (cESC) can only produce somatic cell types. For this reason, cESCs are often considered to be equivalent to mouse EpiSC. To define these cell types more rigorously, we have performed comparative microarray analysis to describe a transcriptomic profile specific for each cell type. This is validated by real time RT-PCR and in situ hybridisation. We find that both cES and cBC cells express classic pluripotency-related genes (including cPOUV/OCT4, NANOG, SOX2/3, KLF2 and SALL4), whereas expression of DAZL, DND1, DDX4 and PIWIL1 defines a molecular signature for germ cells. Surprisingly, contrary to the prevailing view, our results also suggest that cES cells resemble mouse ES cells more closely than mouse EpiSC.
Highlights
•First comparison of transcriptomic contents of avian stem cells•Identification of avian pluripotency associated set of genes•Identification of chicken germ cell specific set of genes•Establishment of similarities between cES and mES cells•Evidence for a heterogeneous molecularly status of the early chicken embryos
doi:10.1016/j.scr.2014.11.005
PMCID: PMC4305369  PMID: 25514344
4.  Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte 
Genome Biology  2014;15(11):493.
Background
Following fertilization, the early proteomes of metazoans are defined by the translation of stored but repressed transcripts; further embryonic development relies on de novo transcription of the zygotic genome. During sexual development of Plasmodium berghei, a rodent model for human malaria species including P. falciparum, the stability of repressed mRNAs requires the translational repressors DOZI and CITH. When these repressors are absent, Plasmodium zygote development and transmission to the mosquito vector is halted, as hundreds of transcripts become destabilized. However, which mRNAs are direct targets of these RNA binding proteins, and thus subject to translational repression, is unknown.
Results
We identify the maternal mRNA contribution to post-fertilization development of P. berghei using RNA immunoprecipitation and microarray analysis. We find that 731 mRNAs, approximately 50% of the transcriptome, are associated with DOZI and CITH, allowing zygote development to proceed in the absence of RNA polymerase II transcription. Using GFP-tagging, we validate the repression phenotype of selected genes and identify mRNAs relying on the 5′ untranslated region for translational control. Gene deletion reveals a novel protein located in the ookinete crystalloid with an essential function for sporozoite development.
Conclusions
Our study details for the first time the P. berghei maternal repressome. This mRNA population provides the developing ookinete with coding potential for key molecules required for life-cycle progression, and that are likely to be critical for the transmission of the malaria parasite from the rodent and the human host to the mosquito vector.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0493-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-014-0493-0
PMCID: PMC4234863  PMID: 25418785
5.  A comprehensive evaluation of rodent malaria parasite genomes and gene expression 
BMC Biology  2014;12(1):86.
Background
Rodent malaria parasites (RMP) are used extensively as models of human malaria. Draft RMP genomes have been published for Plasmodium yoelii, P. berghei ANKA (PbA) and P. chabaudi AS (PcAS). Although availability of these genomes made a significant impact on recent malaria research, these genomes were highly fragmented and were annotated with little manual curation. The fragmented nature of the genomes has hampered genome wide analysis of Plasmodium gene regulation and function.
Results
We have greatly improved the genome assemblies of PbA and PcAS, newly sequenced the virulent parasite P. yoelii YM genome, sequenced additional RMP isolates/lines and have characterized genotypic diversity within RMP species. We have produced RNA-seq data and utilised it to improve gene-model prediction and to provide quantitative, genome-wide, data on gene expression. Comparison of the RMP genomes with the genome of the human malaria parasite P. falciparum and RNA-seq mapping permitted gene annotation at base-pair resolution. Full-length chromosomal annotation permitted a comprehensive classification of all subtelomeric multigene families including the ‘Plasmodium interspersed repeat genes’ (pir). Phylogenetic classification of the pir family, combined with pir expression patterns, indicates functional diversification within this family.
Conclusions
Complete RMP genomes, RNA-seq and genotypic diversity data are excellent and important resources for gene-function and post-genomic analyses and to better interrogate Plasmodium biology. Genotypic diversity between P. chabaudi isolates makes this species an excellent parasite to study genotype-phenotype relationships. The improved classification of multigene families will enhance studies on the role of (variant) exported proteins in virulence and immune evasion/modulation.
Electronic supplementary material
The online version of this article (doi:10.1186/s12915-014-0086-0) contains supplementary material, which is available to authorized users.
doi:10.1186/s12915-014-0086-0
PMCID: PMC4242472  PMID: 25359557
Plasmodium chabaudi; Plasmodium berghei; Plasmodium yoelii; Genomes; RNA-seq; Genotypic diversity; Multigene families; pirs; Phylogeny
6.  Identification of a Novel Conjugative Plasmid in Mycobacteria That Requires Both Type IV and Type VII Secretion 
mBio  2014;5(5):e01744-14.
ABSTRACT
Conjugative plasmids have been identified in a wide variety of different bacteria, ranging from proteobacteria to firmicutes, and conjugation is one of the most efficient routes for horizontal gene transfer. The most widespread mechanism of plasmid conjugation relies on different variants of the type IV secretion pathway. Here, we describe the identification of a novel type of conjugative plasmid that seems to be unique for mycobacteria. Interestingly, while this plasmid is efficiently exchanged between different species of slow-growing mycobacteria, including Mycobacterium tuberculosis, it could not be transferred to any of the fast-growing mycobacteria tested. Genetic analysis of the conjugative plasmid showed the presence of a locus containing homologues of three type IV secretion system components and a relaxase. In addition, a new type VII secretion locus was present. Using transposon insertion mutagenesis, we show that in fact both these secretion systems are essential for conjugation, indicating that this plasmid represents a new class of conjugative plasmids requiring two secretion machineries. This plasmid could form a useful new tool to exchange or introduce DNA in slow-growing mycobacteria.
IMPORTANCE
Conjugative plasmids play an important role in horizontal gene transfer between different bacteria and, as such, in their adaptation and evolution. This effect is most obvious in the spread of antibiotic resistance genes. Thus far, conjugation of natural plasmids has been described only rarely for mycobacterial species. In fact, it is generally accepted that M. tuberculosis does not show any recent sign of horizontal gene transfer. In this study, we describe the identification of a new widespread conjugative plasmid that can also be efficiently transferred to M. tuberculosis. This plasmid therefore poses both a threat and an opportunity. The threat is that, through the acquisition of antibiotic resistance markers, this plasmid could start a rapid spread of antibiotic resistance genes between pathogenic mycobacteria. The opportunity is that we could use this plasmid to generate new tools for the efficient introduction of foreign DNA in slow-growing mycobacteria.
doi:10.1128/mBio.01744-14
PMCID: PMC4173767  PMID: 25249284
7.  A robust SNP barcode for typing Mycobacterium tuberculosis complex strains 
Nature Communications  2014;5:4812.
Strain-specific genomic diversity in the Mycobacterium tuberculosis complex (MTBC) is an important factor in pathogenesis that may affect virulence, transmissibility, host response and emergence of drug resistance. Several systems have been proposed to classify MTBC strains into distinct lineages and families. Here, we investigate single-nucleotide polymorphisms (SNPs) as robust (stable) markers of genetic variation for phylogenetic analysis. We identify ~92k SNP across a global collection of 1,601 genomes. The SNP-based phylogeny is consistent with the gold-standard regions of difference (RD) classification system. Of the ~7k strain-specific SNPs identified, 62 markers are proposed to discriminate known circulating strains. This SNP-based barcode is the first to cover all main lineages, and classifies a greater number of sublineages than current alternatives. It may be used to classify clinical isolates to evaluate tools to control the disease, including therapeutics and vaccines whose effectiveness may vary by strain type.
Genetic variation in Mycobacterium tuberculosis complex (MTBC) bacteria is responsible for differences in factors such as virulence and transmissibility. Here, the authors analyse the genomes of 1,601 MTBC isolates from diverse geographic locations and identify 62 SNPs that may be used to resolve lineages and sublineages of these strains.
doi:10.1038/ncomms5812
PMCID: PMC4166679  PMID: 25176035
12.  Factors Associated with the Seroprevalence of Leishmaniasis in Dogs Living around Atlantic Forest Fragments 
PLoS ONE  2014;9(8):e104003.
Canine visceral leishmaniasis is an important zoonosis in Brazil. However, infection patterns are unknown in some scenarios such as rural settlements around Atlantic Forest fragments. Additionally, controversy remains over risk factors, and most identified patterns of infection in dogs have been found in urban areas. We conducted a cross-sectional epidemiological survey to assess the prevalence of leishmaniasis in dogs through three different serological tests, and interviews with owners to assess features of dogs and households around five Atlantic Forest remnants in southeastern Brazil. We used Generalized Linear Mixed Models and Chi-square tests to detect associations between prevalence and variables that might influence Leishmania infection, and a nearest neighbor dispersion analysis to assess clustering in the spatial distribution of seropositive dogs. Our findings showed an average prevalence of 20% (ranging from 10 to 32%) in dogs. Nearly 40% (ranging from 22 to 55%) of households had at least one seropositive dog. Some individual traits of dogs (height, sterilization, long fur, age class) were found to positively influence the prevalence, while some had negative influence (weight, body score, presence of ectoparasites). Environmental and management features (number of cats in the households, dogs with free-ranging behavior) also entered models as negative associations with seropositivity. Strong and consistent negative (protective) influences of the presence of chickens and pigs in dog seropositivity were detected. Spatial clustering of cases was detected in only one of the five study sites. The results showed that different risk factors than those found in urban areas may drive the prevalence of canine leishmaniasis in farm/forest interfaces, and that humans and wildlife risk infection in these areas. Domestic dog population limitation by gonadectomy, legal restriction of dog numbers per household and owner education are of the greatest importance for the control of visceral leishmaniasis in rural zones near forest fragments.
doi:10.1371/journal.pone.0104003
PMCID: PMC4121198  PMID: 25089629
13.  The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India 
Background
Cholera infection continues to be a threat to global public health. The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century.
Methodology/Principal Findings
Thirty-eight V. cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India were characterised by a combination of microbiology, molecular typing and whole-genome sequencing. The genomic analysis indicated that two clones of V. cholera circulated in the region and caused disease during this time. These clones fell into two distinct sub-clades that map independently onto wave 3 of the phylogenetic tree of seventh pandemic V. cholerae El Tor. Sequence analyses of the cholera toxin gene, the Vibrio seventh Pandemic Island II (VSPII) and SXT element correlated with this phylogenetic position of the two clades on the El Tor tree. The clade 2 isolates, characterized by a drug-resistant profile and the expression of a distinct cholera toxin, are closely related to the recent V. cholerae isolated elsewhere, including Haiti, but fell on a distinct branch of the tree, showing they were independent outbreaks. Multi-Locus Sequence Typing (MLST) distinguishes two sequence types among the 38 isolates, that did not correspond to the clades defined by whole-genome sequencing. Multi-Locus Variable-length tandem-nucleotide repeat Analysis (MLVA) identified 16 distinct clusters.
Conclusions/Significance
The use of whole-genome sequencing enabled the identification of two clones of V. cholerae that circulated during the 2009 Chandigarh outbreak. These clones harboured a similar structure of ICEVchHai1 but differed mainly in the structure of CTX phage and VSPII. The limited capacity of MLST and MLVA to discriminate between the clones that circulated in the 2009 Chandigarh outbreak highlights the value of whole-genome sequencing as a route to the identification of further genetic markers to subtype V. cholerae isolates.
Author Summary
Vibrio cholerae is a diarrheal pathogen that is responsible for substantial morbidity and mortality worldwide. Historically, seven pandemics of cholera have been recognized, with classical biotype strains associated with the sixth and the El Tor biotype with the seventh (current) pandemic. Recently multi-drug resistant El Tor variants expressing classical cholera toxin have replaced the original El Tor strains in many epidemics, and are sometimes associated with more severe diarrhea leading to a higher mortality rate. In regions that experience recurrent cholera outbreaks, such as Northern India, it is important to understand the nature of the circulating strains and establish how they are related to the strains circulating globally. Here, we have demonstrated that whole- genome sequencing is a valuable method to characterize V. cholerae isolates that circulated during the 2009 outbreak in the Northern Indian city of Chandigarh. Through comparative genomic analysis, we identified two clones that circulated during a single outbreak. Importantly, these clones contain significant differences in the structure of the cholera toxin gene and the Vibrio seventh pandemic island II. Our findings demonstrate the limitations of current molecular typing techniques and the importance of surveillance with whole-genome sequencing for identifying V. cholerae clades with distinct genomic signatures.
doi:10.1371/journal.pntd.0002981
PMCID: PMC4109905  PMID: 25058483
14.  Genome Sequences of the Oxytetracycline Production Strain Streptomyces rimosus R6-500 and Two Mutants with Chromosomal Rearrangements 
Genome Announcements  2014;2(4):e00517-14.
The genome sequence of Streptomyces rimosus R6-500, an industrially improved strain which produces high titers of the important antibiotic oxytetracycline, is reported, as well as the genome sequences of two derivatives arising due to the genetic instability of the strain.
doi:10.1128/genomeA.00517-14
PMCID: PMC4102857  PMID: 25035320
15.  Genome-wide Functional Analysis of Plasmodium Protein Phosphatases Reveals Key Regulators of Parasite Development and Differentiation 
Cell Host & Microbe  2014;16(1):128-140.
Summary
Reversible protein phosphorylation regulated by kinases and phosphatases controls many cellular processes. Although essential functions for the malaria parasite kinome have been reported, the roles of most protein phosphatases (PPs) during Plasmodium development are unknown. We report a functional analysis of the Plasmodium berghei protein phosphatome, which exhibits high conservation with the P. falciparum phosphatome and comprises 30 predicted PPs with differential and distinct expression patterns during various stages of the life cycle. Gene disruption analysis of P. berghei PPs reveals that half of the genes are likely essential for asexual blood stage development, whereas six are required for sexual development/sporogony in mosquitoes. Phenotypic screening coupled with transcriptome sequencing unveiled morphological changes and altered gene expression in deletion mutants of two N-myristoylated PPs. These findings provide systematic functional analyses of PPs in Plasmodium, identify how phosphatases regulate parasite development and differentiation, and can inform the identification of drug targets for malaria.
Graphical Abstract
Highlights
•Phylogenetic analysis identifies 30 Plasmodium berghei protein phosphatases (PPs)•Functional analysis reveals role for six PPs in sexual development/sporogony•Two N-myristoylated PPs play key roles in sex allocation and parasite transmission•RNA-Seq highlights significantly altered gene clusters in the N-myristoylated PP mutants
Protein phosphorylation regulated by kinases and phosphatases plays important roles in the Plasmodium life cycle. By performing a genome-wide functional screen, Guttery et al. examine protein phosphatases in Plasmodium berghei and identify phosphatases likely essential for asexual development in host blood as well as those required for sexual/sporogony development in mosquitos.
doi:10.1016/j.chom.2014.05.020
PMCID: PMC4094981  PMID: 25011111
16.  Recombinations in Staphylococcal Cassette Chromosome mec Elements Compromise the Molecular Detection of Methicillin Resistance in Staphylococcus aureus 
PLoS ONE  2014;9(6):e101419.
Clinical laboratories are increasingly using molecular tests for methicillin-resistant Staphylococcus aureus (MRSA) screening. However, primers have to be targeted to a variable chromosomal region, the staphylococcal cassette chromosome mec (SCCmec). We initially screened 726 MRSA isolates from a single UK hospital trust by recombinase polymerase amplification (RPA), a novel, isothermal alternative to PCR. Undetected isolates were further characterised using multilocus sequence, spa typing and whole genome sequencing. 96% of our tested phenotypically MRSA isolates contained one of the six orfX-SCCmec junctions our RPA test and commercially available molecular tests target. However 30 isolates could not be detected. Sequencing of 24 of these isolates demonstrated recombinations within the SCCmec element with novel insertions that interfered with the RPA, preventing identification as MRSA. This result suggests that clinical laboratories cannot rely solely upon molecular assays to reliably detect all methicillin-resistance. The presence of significant recombinations in the SCCmec element, where the majority of assays target their primers, suggests that there will continue to be isolates that escape identification. We caution that dependence on amplification-based molecular assays will continue to result in failure to diagnose a small proportion (∼4%) of MRSA isolates, unless the true level of SCCmec natural diversity is determined by whole genome sequencing of a large collection of MRSA isolates.
doi:10.1371/journal.pone.0101419
PMCID: PMC4074205  PMID: 24972080
17.  Short Communication: Effect of Short-Course Antenatal Zidovudine and Single-Dose Nevirapine on the BED Capture Enzyme Immunoassay Levels in HIV Type 1 Subtype C Infection 
Abstract
Cross-sectional prevalence studies based on immunoassays that discriminate between recent and long-term infections, such as the BED assay, have been widely used to estimate HIV incidence. However, individuals receiving highly active antiretroviral therapy tend to have lower BED levels and are associated with a higher risk for being mistakenly classified as recent infections. To assess the effect of short-term antenatal zidovudine (ZDV) and single-dose nevirapine (sdNVP) on the BED levels in HIV-1C infection, we measured longitudinal BED normalized optical density (OD-n) levels using stored plasma samples collected prenatally and postnatally from 159 pregnant HIV-infected women in Botswana who participated in the randomized clinical Mother-to-Child-Prevention study, the Mashi study. All women received ZDV from 34 weeks gestation through delivery and were randomized to receive either sdNVP or placebo during labor. Among 159 subjects, the OD-n levels decreased from baseline to delivery in 93 subjects (p=0.039), suggesting that short-course ZDV may decrease OD-n levels. sdNVP at delivery did not affect longitudinal BED OD-n levels postdelivery. However, sdNVP appeared to modify the association between CD4 count at delivery and OD-n levels postdelivery. When estimating HIV incidence with the BED assay, special care may be required regarding women who received short-term ZDV for prevention of mother-to-child transmission.
doi:10.1089/aid.2012.0294
PMCID: PMC3653368  PMID: 23521375
19.  The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host–parasite interaction 
Nucleic Acids Research  2014;42(11):7113-7131.
Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5′ ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct.
doi:10.1093/nar/gku322
PMCID: PMC4066756  PMID: 24799432
20.  PolyTB: A genomic variation map for Mycobacterium tuberculosis 
Summary
Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is the second major cause of death from an infectious disease worldwide. Recent advances in DNA sequencing are leading to the ability to generate whole genome information in clinical isolates of M. tuberculosis complex (MTBC). The identification of informative genetic variants such as phylogenetic markers and those associated with drug resistance or virulence will help barcode Mtb in the context of epidemiological, diagnostic and clinical studies. Mtb genomic datasets are increasingly available as raw sequences, which are potentially difficult and computer intensive to process, and compare across studies. Here we have processed the raw sequence data (>1500 isolates, eight studies) to compile a catalogue of SNPs (n = 74,039, 63% non-synonymous, 51.1% in more than one isolate, i.e. non-private), small indels (n = 4810) and larger structural variants (n = 800). We have developed the PolyTB web-based tool (http://pathogenseq.lshtm.ac.uk/polytb) to visualise the resulting variation and important meta-data (e.g. in silico inferred strain-types, location) within geographical map and phylogenetic views. This resource will allow researchers to identify polymorphisms within candidate genes of interest, as well as examine the genomic diversity and distribution of strains. PolyTB source code is freely available to researchers wishing to develop similar tools for their pathogen of interest.
doi:10.1016/j.tube.2014.02.005
PMCID: PMC4066953  PMID: 24637013
Mycobacterium tuberculosis; Database; Genomics; Software; Molecular epidemiology; Whole-genome sequencing
21.  Ionizing radiation-induced metabolic oxidative stress and prolonged cell injury 
Cancer letters  2011;327(0):48-60.
Cellular exposure to ionizing radiation leads to oxidizing events that alter atomic structure through direct interactions of radiation with target macromolecules or via products of water radiolysis. Further, the oxidative damage may spread from the targeted to neighboring, non-targeted bystander cells through redox-modulated intercellular communication mechanisms. To cope with the induced stress and the changes in the redox environment, organisms elicit transient responses at the molecular, cellular and tissue levels to counteract toxic effects of radiation. Metabolic pathways are induced during and shortly after the exposure. Depending on radiation dose, dose-rate and quality, these protective mechanisms may or may not be sufficient to cope with the stress. When the harmful effects exceed those of homeostatic biochemical processes, induced biological changes persist and may be propagated to progeny cells. Physiological levels of reactive oxygen and nitrogen species play critical roles in many cellular functions. In irradiated cells, levels of these reactive species may be increased due to perturbations in oxidative metabolism and chronic inflammatory responses, thereby contributing to the long-term effects of exposure to ionizing radiation on genomic stability. Here, in addition to immediate biological effects of water radiolysis on DNA damage, we also discuss the role of mitochondria in the delayed outcomes of ionization radiation. Defects in mitochondrial functions lead to accelerated aging and numerous pathological conditions. Different types of radiation vary in their linear energy transfer (LET) properties, and we discuss their effects on various aspects of mitochondrial physiology. These include short and long-term in vitro and in vivo effects on mitochondrial DNA, mitochondrial protein import and metabolic and antioxidant enzymes.
doi:10.1016/j.canlet.2011.12.012
PMCID: PMC3980444  PMID: 22182453
Ionizing radiation; Reactive oxygen/nitrogen species; Oxidative metabolism; Mitochondria; Genomic instability; adaptive responses; bystander effects
22.  SVAMP: sequence variation analysis, maps and phylogeny 
Bioinformatics  2014;30(15):2227-2229.
Summary: SVAMP is a stand-alone desktop application to visualize genomic variants (in variant call format) in the context of geographical metadata. Users of SVAMP are able to generate phylogenetic trees and perform principal coordinate analysis in real time from variant call format (VCF) and associated metadata files. Allele frequency map, geographical map of isolates, Tajima’s D metric, single nucleotide polymorphism density, GC and variation density are also available for visualization in real time. We demonstrate the utility of SVAMP in tracking a methicillin-resistant Staphylococcus aureus outbreak from published next-generation sequencing data across 15 countries. We also demonstrate the scalability and accuracy of our software on 245 Plasmodium falciparum malaria isolates from three continents.
Availability and implementation: The Qt/C++ software code, binaries, user manual and example datasets are available at http://cbrc.kaust.edu.sa/svamp
Contact: arnab.pain@kaust.edu.sa or arnab.pain@cantab.net
Supplementary information: Supplementary data are available at Bioinformatics online.
doi:10.1093/bioinformatics/btu176
PMCID: PMC4103593  PMID: 24700318
23.  The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode 
Genome Biology  2014;15(3):R43.
Background
Globodera pallida is a devastating pathogen of potato crops, making it one of the most economically important plant parasitic nematodes. It is also an important model for the biology of cyst nematodes. Cyst nematodes and root-knot nematodes are the two most important plant parasitic nematode groups and together represent a global threat to food security.
Results
We present the complete genome sequence of G. pallida, together with transcriptomic data from most of the nematode life cycle, particularly focusing on the life cycle stages involved in root invasion and establishment of the biotrophic feeding site. Despite the relatively close phylogenetic relationship with root-knot nematodes, we describe a very different gene family content between the two groups and in particular extensive differences in the repertoire of effectors, including an enormous expansion of the SPRY domain protein family in G. pallida, which includes the SPRYSEC family of effectors. This highlights the distinct biology of cyst nematodes compared to the root-knot nematodes that were, until now, the only sedentary plant parasitic nematodes for which genome information was available. We also present in-depth descriptions of the repertoires of other genes likely to be important in understanding the unique biology of cyst nematodes and of potential drug targets and other targets for their control.
Conclusions
The data and analyses we present will be central in exploiting post-genomic approaches in the development of much-needed novel strategies for the control of G. pallida and related pathogens.
doi:10.1186/gb-2014-15-3-r43
PMCID: PMC4054857  PMID: 24580726
24.  Pilomyxoid astrocytoma of the cerebellar vermis in an elderly patient 
Background:
Pilomyxoid astrocytoma (PMA) has recently been accepted as an aggressive variant of pilocytic astrocytoma with distinct histopathological features. PMAs have been frequently described in the pediatric population with a predilection for the hypothalamic/chiasmatic region.
Case Description:
A 72-year-old African American male presented with 6 months of memory loss, difficulty expressing himself, and a progressively worsening gait. Magnetic resonance imaging of the brain demonstrated a heterogeneously enhancing cystic mass centered within the cerebellar vermis with mass effect on the fourth ventricle and ventriculomegaly. The patient underwent placement of a ventriculoperitoneal shunt followed by a surgical resection of the lesion, which after immunohistopathologic evaluation, was diagnosed as a World Health Organization grade II PMA. The patient refused further treatment of the lesion and expired 11 months after initial symptom presentation and 4 months after surgery.
Conclusion:
To our knowledge, this is the first report of PMA of the cerebellar vermis in a previously unreported age group. This case report describes the natural history of this type of tumor in a patient who refused adjuvant therapy following surgical resection.
doi:10.4103/2152-7806.127968
PMCID: PMC3994688  PMID: 24778917
Cerebellar vermis; elderly patient; natural history; pilomyxoid astrocytoma
25.  Assembly of the Genome of the Disease Vector Aedes aegypti onto a Genetic Linkage Map Allows Mapping of Genes Affecting Disease Transmission 
The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled — there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait.
Author Summary
Mosquitoes are important for transmission of human diseases including dengue and yellow fever. The sequencing of the genomes of key mosquito species including Aedes aegypti has helped us to understand the factors that allow mosquitoes to vector disease. While the genome for Ae. aegypti has been sequenced, it is in many pieces which have not yet been arranged on chromosomes. To this end, we have created a genetic linkage map and measured the distance between genetic markers, which allows us to assign them to regions of the genome. Using this method, we also detected errors in the current genome sequences. We used our genetic map to find regions of the mosquito genome associated with the development of Brugia malayi, a nematode that causes lymphatic filariasis in humans. A better genome assembly will be important for the development of novel methods for controlling disease transmission.
doi:10.1371/journal.pntd.0002652
PMCID: PMC3907309  PMID: 24498447

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