Genetic structure and male-mediated gene flow in the ghost bat (Macroderma gigas)

The Australian ghost bat is a large, opportunistic carnivorous species that has undergone a marked range contraction toward more mesic, tropical sites over the past century. Comparison of mitochondrial DNA (mtDNA) control region sequences and six nuclear microsatellite loci in 217 ghost bats from nine populations across subtropical and tropical Australia revealed strong population subdivision (mtDNA phi(ST) = 0.80; microsatellites URST = 0.337). Low-latitude (tropical) populations had higher heterozygosity and less marked phylogeographic structure and lower subdivision among sites within regions (within Northern Territory [NT] and within North Queensland [NQ]) than did populations at higher latitudes (subtropical sites; central Queensland [CQ]), although sampling of geographically proximal breeding sites is unavoidably restricted for the latter. Gene flow among populations within each of the northern regions appears to be male biased in that the difference in population subdivision for mtDNA and microsatellites (NT phi(ST) = 0.39, URST = 0.02; NQ phi(ST) = 0.60, URST = -0.03) is greater than expected from differences in the effective population size of haploid versus diploid loci. The high level of population subdivision across the range of the ghost bat contrasts with evidence for high gene flow in other chiropteran species and may be due to narrow physiological tolerances and consequent limited availability of roosts for ghost bats, particularly across the subtropical and relatively arid regions. This observation is consistent with the hypothesis that the contraction of the species' range is associated with late Holocene climate change. The extreme isolation among higher-latitude populations may predispose them to additional local extinctions if the processes responsible for the range contraction continue to operate.

Nanotossicologia dei quantum dot di CdS in linee cellulari umane

Le nanotecnologie sono un settore emergente in rapida crescita, come dimostra l'esplosione del mercato dei prodotti ad esso collegati. I quantum dot di cadmio solfuro (CdS QD) sono ampiamente utilizzati per la produzione di materiali semiconduttori e dispositivi optoelettronici; tuttavia, non sono ancora completamente chiari gli effetti di questi nanomateriali sulla salute umana. Questo lavoro di dottorato si pone l'obbiettivo di definire il potenziale citotossico e genotossico dei CdS QD in linee cellulari umane e definirne il meccanismo implicato. A questo scopo, essendo il fegato uno dei principali organi di accumulo del cadmio e dei nanomateriali a base di cadmio, è stata utilizzata la linea cellulare HepG2 derivante da un epatocarcinoma umano. È stato evidenziato, in seguito all'assorbimento, da parte delle cellule, dei CdS QD, un effetto citotossico, con conseguente modulazione dell'espressione genica di una serie di geni coinvolti sia nei processi di rescue (autofagia, risposta allo stress) sia in quelli di morte cellulare programmata. È stato, inoltre, dimostrata l'assenza di un rilevante effetto genotossico dipendente da questi nanomateriali. Infine, è stato osservato che cellule esposte ai CdS QD presentano mitocondri con un potenziale di membrana alterato, con conseguente alterazione della funzionalità di tale organello, pur conservando l'integrità del DNA mitocondriale.

Biomarkers

Introduction – Why do we need ‘biomarkers? Biomarkers of protein oxidation Introduction Major issues/questions Protein carbonyl biomarkers Biochemistry Methods of measurement Storage, stability and limitations in use Protein thiol biomarkers Biochemistry Methods of measurement Storage, stability and limitations on use Aliphatic amino acid biomarkers Biochemistry Methods of measurement Storage, stability and limitations on use Oxidised Tryptophan Biomarkers Biochemistry Method of measurement Storage, stability and limitations on use Oxidised tyrosine biomarkers Biochemistry Methods of measurement Storage, stability and limitations on use Formation of neoepitopes on oxidised proteins Validation of assays for protein oxidation biomarkers Relationship of protein oxidation to disease Modulation of protein oxidation biomarkers by antioxidants Future perspectives Introduction to lipid peroxidation biomarkers Introduction: biochemistry of lipid peroxidation Malondialdehyde Methods of measurement Storage, stability and limitations on use Conjugated dienes Method of measurement Storage, stability and limitations of use LDL lag phase Method of measurement Storage, stability and limitations of use Hydrocarbon gases Biochemistry Method of measurement Storage, stability and limitations on use Lipofuscin Biochemistry Method of measurement Storage, stability and limitation on use Lipid peroxides Biochemistry Method of measurement Storage, stability and limitations on use Isoprostanes Biochemistry Method of measurement Storage, stability and limitations on use Possible new biomarkers of lipid oxidation Relationship of lipid peroxidation to disease Modulation of lipid peroxidation biomarkers by antioxidants Functional consequences of lipid peroxidation Contribution of dietary intake to lipid peroxidation products Biomarkers of DNA oxidation Introduction Confounding factors Units and terminology Nuclear and mitochondrial DNA damage Lymphocytes as surrogate tissues Measurement of DNA damage with the comet assay Practical details Storage, stability, and limitations of the assay Measurement of DNA base oxidation by HPLC Practical details Storage, stability and limitations of the method Measurement of DNA base oxidation by GC–MS Biochemistry of 8-oxoguanine, adenine and fapy derivatives Methods of measurement Storage, stability and limitations of the method Analysis of guanine oxidation products in urine Method of measurement Limitations and criticisms Immunochemical methods Methods of measurement Storage, stability, and limitations of the assay 32P post-labelling Method of measurement Limitations and criticisms Validation of assays for DNA oxidation Oxo-dGuo in lymphocyte DNA Urinary measurements DNA–aldehyde adducts Biochemistry Method of measurement Products of reactive nitrogen species Endpoints arising from oxidative DNA damage Mutations Chromosome aberrations Micronuclei Site-specific DNA damage Relationship of DNA oxidation to disease Modulation of DNA oxidation biomarkers by antioxidants Direct and indirect effects of oxidative stress: measures of total oxidant/antioxidant levels Visualisation of cellular oxidants Biochemistry: histochemical detection of ROS Method of measurement Limitations, storage and stability Measurement of hydrogen peroxide Biochemistry Methods of measurement Storage, stability and limitations on use Measurement of the ratio of antioxidant/oxidised antioxidant Biochemistry Method of measurement Storage, stability and limitations on use Total antioxidant capacity Biochemistry Terminology Methods of measurement Storage, stability and limitations on use Validation of assays for direct oxidant and antioxidant biomarkers Relationship of oxidant/antioxidant measurement to disease Modulation of oxidant/antioxidant biomarkers by dietary antioxidants Induction of genes in response to oxidative stress Background Measurement of antioxidant responsive genes and proteins Effects of antioxidant intake on the activity of antioxidant enzymes

Prenatal environmental exposure and neurodevelopmentally important gene expression in malformed brain tissue from pediatric intractable epilepsy patients

The primary objective of this proposal was to determine whether mitochondrial oxidative stress and variation in a particular mtDNA lineage contribute to the risk of developing cortical dysplasia and are potential contributing factors in epileptogenesis in children. The occurrence of epilepsy in children is highly associated with malformations of cortical development (MCD). It appears that MCD might arise from developmental errors due to environmental exposures in combination with inherited variation in response to environmental exposures and mitochondrial function. Therefore, it is postulated that variation in a particular mtDNA lineage of children contributes to the effects of mitochondrial DNA damage on MCD phenotype. Quantitative PCR and dot blot were used to examine mitochondrial oxidative damage and single nucleotide polymorphism (SNP) in the mitochondrial genome in brain tissue from 48 pediatric intractable epilepsy patients from Miami Children’s Hospital and 11 control samples from NICHD Brain and Tissue Bank for Developmental Disorders. Epilepsy patients showed higher mtDNA copy number compared to normal health subjects (controls). Oxidative mtDNA damage was lower in non-neoplastic but higher in neoplastic epilepsy patients compared to controls. There was a trend of lower mtDNA oxidative damage in the non-neoplastic (MCD) patients compared to controls, yet, the reverse was observed in neoplastic (MCD and Non-MCD) epilepsy patients. The presence of mtDNA SNP and haplogroups did not show any statistically significant relationships with epilepsy phenotypes. However, SNPs G9804A and G9952A were found in higher frequencies in epilepsy samples. Logistic regression analysis showed no relationship between mtDNA oxidative stress, mtDNA copy number, mitochondrial haplogroups and SNP variations with epilepsy in pediatric patients. The levels of mtDNA copy number and oxidative mtDNA damage and the SNPs G9952A and T10010C predicted neoplastic epilepsy, however, this was not significant due to a small sample size of pediatric subjects. Findings of this study indicate that an increase in mtDNA content may be compensatory mechanisms for defective mitochondria in intractable epilepsy and brain tumor. Further validation of these findings related to mitochondrial genotypes and mitochondrial dysfunction in pediatric epilepsy and MCD may lay the ground for the development of new therapies and prevention strategies during embryogenesis.

Long-finned pilot whale population diversity and structure in Atlantic waters assessed through biogeochemical and genetic markers

Acknowledgements. Cetacean samples were collected under the auspices of stranding monitoring programs run by the Sociedade Portuguesa de Vida Selvagem, the Coordinadora para o Estudio dos Mamíferos Mariños (supported by the regional government Xunta de Galicia), the UK Cetacean Strandings Investigation Programme and the Scottish Agriculture College Veterinary Science Division (jointly funded by Defra and the Devolved Governments of Scotland and Wales), the Marine Mammals Research Group of the Institute of Marine Research (Norway), the Museum of Natural History of the Faroe Islands and the International Fund for Animal Welfare Marine Mammal Rescue and Research Program (USA). The authors thank all the members of these institutions and organizations for their assistance with data and sample collection. S.S.M., P.M.F. and M.F. were supported by PhD grants from the Fundação para a Ciência e Tecnologia (POPH/FSE ref SFRH/BD/ 38735/ 2007, SFRH/BD/36766/2007 and SFRH/BD/30240/ 2006, respectively). A.L. was supported by a postdoctoral grant from the Fundação para a Ciência e Tecnologia (ref SFRH/BPD/82407/2011). The work related to strandings and tissue collection in Portugal was partially supported by the SafeSea project EEAGrants PT 0039 (supported by Iceland, Liechtenstein and Norway through the EEA Financial Mechanism), the MarPro project Life09 NAT/PT/000038 (funded by the European Union program LIFE+) and the project CetSenti FCT RECI/AAG-GLO/0470/2012 (FCOMP- 01-0124-FEDER-027472) (funded by the program COMPETE and the Fundação para a Ciência e Tecnologia). G.J.P. thanks the University of Aveiro and Caixa Geral de Depósitos (Portugal) for financial support. The authors acknowledge the assistance of the chemical analysts at Marine Scotland Science with the fatty acid analysis.

Long-finned pilot whale population diversity and structure in Atlantic waters assessed through biogeochemical and genetic markers

Acknowledgements. Cetacean samples were collected under the auspices of stranding monitoring programs run by the Sociedade Portuguesa de Vida Selvagem, the Coordinadora para o Estudio dos Mamíferos Mariños (supported by the regional government Xunta de Galicia), the UK Cetacean Strandings Investigation Programme and the Scottish Agriculture College Veterinary Science Division (jointly funded by Defra and the Devolved Governments of Scotland and Wales), the Marine Mammals Research Group of the Institute of Marine Research (Norway), the Museum of Natural History of the Faroe Islands and the International Fund for Animal Welfare Marine Mammal Rescue and Research Program (USA). The authors thank all the members of these institutions and organizations for their assistance with data and sample collection. S.S.M., P.M.F. and M.F. were supported by PhD grants from the Fundação para a Ciência e Tecnologia (POPH/FSE ref SFRH/BD/ 38735/ 2007, SFRH/BD/36766/2007 and SFRH/BD/30240/ 2006, respectively). A.L. was supported by a postdoctoral grant from the Fundação para a Ciência e Tecnologia (ref SFRH/BPD/82407/2011). The work related to strandings and tissue collection in Portugal was partially supported by the SafeSea project EEAGrants PT 0039 (supported by Iceland, Liechtenstein and Norway through the EEA Financial Mechanism), the MarPro project Life09 NAT/PT/000038 (funded by the European Union program LIFE+) and the project CetSenti FCT RECI/AAG-GLO/0470/2012 (FCOMP- 01-0124-FEDER-027472) (funded by the program COMPETE and the Fundação para a Ciência e Tecnologia). G.J.P. thanks the University of Aveiro and Caixa Geral de Depósitos (Portugal) for financial support. The authors acknowledge the assistance of the chemical analysts at Marine Scotland Science with the fatty acid analysis.

Evaluating demographic models for goat domestication using mtDNA sequences

Routes of migration and exchange are important factors in the debate about how the Neolithic transition spread into Europe. Studying the genetic diversity of livestock can help in tracing back some of these past events. Notably, domestic goat (Capra hircus) did not have any wild progenitors (Capra aegagrus) in Europe before their arrival from the Near East. Studies of mitochondrial DNA have shown that the diversity in European domesticated goats is a subset of that in the wild, underlining the ancestral relationship between both populations. Additionally, an ancient DNA study on Neolithic goat remains has indicated that a high level of genetic diversity was already present early in the Neolithic in northwestern Mediterranean sites. We used coalescent simulations and approximate Bayesian computation, conditioned on patterns of modern and ancient mitochondrial DNA diversity in domesticated and wild goats, to test a series of simplified models of the goat domestication process. Specifically, we ask if domestic goats descend from populations that were distinct prior to domestication. Although the models we present require further analyses, preliminary results indicate that wild and domestic goats are more likely to descend from a single ancestral wild population that was managed 11,500 years before present, and that serial founding events characterise the spread of Capra hircus into Europe.

Genomic and archaeological evidence suggest a dual origin of domestic dogs

The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.

Genetic evidence supports recolonisation by Mya arenaria of western Europe from North America

The softshell clam Mya arenaria (L.) is currently widespread on the east and west coasts of North America. This bivalve also occurs on western European shores, where the post-Pleistocene origin of the species, whether introduced or relict, has been debated. We collected 320 M. arenaria from 8 locations in Europe and North America. Clams (n = 84) from 7 of the locations were examined for mitochondrial DNA variation by sequencing a section of the cytochrome oxidase 1 (COX1) gene. These were analysed together with 212 sequences, sourced from GenBank, from the same gene from 12 additional locations, chiefly from eastern North America but also 1 site each from western North America and from western Europe. Ten microsatellite loci were also investigated in all 320 clams. Nuclear markers showed reduced levels of variation in certain European samples. The same common COX1 haplotypes and microsatellite alleles were present throughout the range of M. arenaria, although significant differences were identified in haplotypic and allelic composition between many samples, particularly those from the 2 continents (Europe and North America). These findings support the hypothesis of post-Pleistocene colonisation of European shores from eastern North America (and the recorded human transfer of clams from the east to the west coast of North America in the 19th century).

Genetic characterization of hawksbill juveniles foraging at Cape Verde islands indicates major undiscovered nesting populations in the region

[EN] The hawksbill sea turtle (Eretmochelys imbricata) is a circumglobal tropical species listed as Critically Endangered by the IUCN. While it is known that at least one stock occurs around the rookeries of São Tome and Principe and Bioko Islands, the eastern Atlantic remains genetically unexplored. We present the first analysis of mitochondrial DNA (mtDNA) sequences (n = 28) of hawksbill juveniles in a foraging aggregation at the Cape Verde Islands, an archipelago located in the eastern Atlantic. The mean size (minimun curve carapace length) of the studied individuals was 42.45 cm.

Genetic characterization of eastern Atlantic hawksbill turtles at a foraging group indicates major undiscovered nesting populations in the region

[EN] Despite the considerable population genetic and connectivity research on the hawksbill sea turtle (Eretmochelys imbricata) and the species being critically endangered, the eastern Atlantic remains understudied. We present the first analysis of mitochondrial DNA (mtDNA) sequences (n = 28) of hawksbill juveniles in a foraging aggregation at the Cape Verde Islands. Our results showed three haplotypes non-reported in any nesting population to date, with one of them accounting for 68% of the samples. These three haplotypes were closely related to each other but highly divergent from all known Caribbean and Western Atlantic haplotypes.

Molecular Taxonomy of Deep Sea Fishes Off the southern coast of India

CMFRI,

Origin and dispersal routes of foreign green and Kemp's ridley turtles in Spanish Atlantic and Mediterranean waters

[EN] The presence of the green and Kemp's ridley turtles is rare at Atlantic and Mediterranean Spanish waters, but the records have increased during the last decades. We reported a new set of records and reviewed all the historical observations of these species. The analysis of a mitochondrial DNA fragment of the newest records provided insights about the origin of the individuals. The Kemp's ridley turtles arrived from the western Atlantic nesting beaches, although the discovering of a new haplotype suggested the existence of an unknown or low sampled nesting area of origin.

Plasmopara sphagneticolae sp. nov. (Peronosporales) on Sphagneticola (Asteraceae) in Australia

A specimen of downy mildew on leaves of Sphagneticola trilobata found in northern Queensland was identified by a systematic approach as a novel species of Plasmopara. A new species, Plasmopara sphagneticolae, is proposed for this specimen, which differs from other species of Plasmopara by morphology, host range, and sequence data from nuclear-ribosomal DNA and mitochondrial DNA. Plasmopara sphagneticolae, together with P. halstedii, are downy mildews found on host species in the tribe Heliantheae (Asteraceae). Plasmopara halstedii causes downy mildew on Helianthus annuus, and is not present on sunflower in Australia. Phylogenetic analysis of the large subunit region of ribosomal DNA showed that P. sphagneticolae was sister to P. halstedii on sunflower.

Soybean Stem Fly, Melanagromyza sojae (Diptera: Agromyzidae), in the New World: detection of high genetic diversity from soybean fields in Brazil

Soybean Stem Fly (SSF), Melanagromyza sojae (Zehntner), belongs to the family Agromyzidae and is highly polyphagous, attacking many plant species of the family Fabaceae, including soybean and other beans. SSF is regarded as one of the most important pests in soybean fields of Asia (e.g., China, India), North East Africa (e.g., Egypt), parts of Russia, and South East Asia. Despite reports of Agromyzidae flies infesting soybean fields in Rio Grande do Sul State (Brazil) in 1983 and 2009 and periodic interceptions of SSF since the 1940s by the USA quarantine authorities, SSF has not been officially reported to have successfully established in the North and South Americas. In South America, M. sojae was recently confirmed using morphology and its complete mitochondrial DNA (mtDNA) was characterized. In the present study, we surveyed the genetic diversity of M. sojae, collected directly from soybean host plants, using partial mtDNA cytochrome oxidase I (COI) gene, and provide evidence of multiple (>10) maternal lineages in SSF populations in South America, potentially representing multiple incursion events. However, a single incursion involving multiple-female founders could not be ruled out. We identified a haplotype that was common in the fields of two Brazilian states and the individuals collected from Australia in 2013. The implications of SSF incursions in southern Brazil are discussed in relation to the current soybean agricultural practices, highlighting an urgent need for better understanding of SSF population movements in the New World, which is necessary for developing effective management options for this significant soybean pest. © FUNPEC-RP.