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1.
Proc Natl Acad Sci U S A ; 119(8)2022 02 22.
Artículo en Inglés | MEDLINE | ID: mdl-35131896

RESUMEN

Orkney was a major cultural center during the Neolithic, 3800 to 2500 BC. Farming flourished, permanent stone settlements and chambered tombs were constructed, and long-range contacts were sustained. From ∼3200 BC, the number, density, and extravagance of settlements increased, and new ceremonial monuments and ceramic styles, possibly originating in Orkney, spread across Britain and Ireland. By ∼2800 BC, this phenomenon was waning, although Neolithic traditions persisted to at least 2500 BC. Unlike elsewhere in Britain, there is little material evidence to suggest a Beaker presence, suggesting that Orkney may have developed along an insular trajectory during the second millennium BC. We tested this by comparing new genomic evidence from 22 Bronze Age and 3 Iron Age burials in northwest Orkney with Neolithic burials from across the archipelago. We identified signals of inward migration on a scale unsuspected from the archaeological record: As elsewhere in Bronze Age Britain, much of the population displayed significant genome-wide ancestry deriving ultimately from the Pontic-Caspian Steppe. However, uniquely in northern and central Europe, most of the male lineages were inherited from the local Neolithic. This suggests that some male descendants of Neolithic Orkney may have remained distinct well into the Bronze Age, although there are signs that this had dwindled by the Iron Age. Furthermore, although the majority of mitochondrial DNA lineages evidently arrived afresh with the Bronze Age, we also find evidence for continuity in the female line of descent from Mesolithic Britain into the Bronze Age and even to the present day.


Asunto(s)
ADN Mitocondrial/genética , Migración Humana/historia , Herencia Paterna/genética , Arqueología , ADN Antiguo/análisis , Inglaterra , Europa (Continente) , Femenino , Fósiles , Pool de Genes , Genoma Humano/genética , Genómica , Haplotipos , Historia Antigua , Historia Medieval , Humanos , Irlanda , Masculino , Escocia
2.
Mol Biol Evol ; 38(10): 4388-4402, 2021 09 27.
Artículo en Inglés | MEDLINE | ID: mdl-34157721

RESUMEN

Dissecting the link between genetic variation and adaptive phenotypes provides outstanding opportunities to understand fundamental evolutionary processes. Here, we use a museomics approach to investigate the genetic basis and evolution of winter coat coloration morphs in least weasels (Mustela nivalis), a repeated adaptation for camouflage in mammals with seasonal pelage color moults across regions with varying winter snow. Whole-genome sequence data were obtained from biological collections and mapped onto a newly assembled reference genome for the species. Sampling represented two replicate transition zones between nivalis and vulgaris coloration morphs in Europe, which typically develop white or brown winter coats, respectively. Population analyses showed that the morph distribution across transition zones is not a by-product of historical structure. Association scans linked a 200-kb genomic region to coloration morph, which was validated by genotyping museum specimens from intermorph experimental crosses. Genotyping the wild populations narrowed down the association to pigmentation gene MC1R and pinpointed a candidate amino acid change cosegregating with coloration morph. This polymorphism replaces an ancestral leucine residue by lysine at the start of the first extracellular loop of the protein in the vulgaris morph. A selective sweep signature overlapped the association region in vulgaris, suggesting that past adaptation favored winter-brown morphs and can anchor future adaptive responses to decreasing winter snow. Using biological collections as valuable resources to study natural adaptations, our study showed a new evolutionary route generating winter color variation in mammals and that seasonal camouflage can be modulated by changes at single key genes.


Asunto(s)
Mustelidae , Pigmentación , Animales , Mamíferos , Mustelidae/fisiología , Fenotipo , Pigmentación/genética , Estaciones del Año
3.
BMC Genomics ; 21(1): 241, 2020 Mar 18.
Artículo en Inglés | MEDLINE | ID: mdl-32183700

RESUMEN

BACKGROUND: Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. RESULTS: Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086. CONCLUSION: Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.


Asunto(s)
Murinae/genética , Animales , Secuencia de Bases , Evolución Biológica , Ratones , Murinae/clasificación , Filogenia , Polonia , Población , Análisis de Secuencia de ADN , Especificidad de la Especie
4.
Mol Biol Evol ; 35(10): 2499-2511, 2018 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-30169693

RESUMEN

Choanoflagellates and filastereans are the closest known single celled relatives of Metazoa within Holozoa and provide insight into how animals evolved from their unicellular ancestors. Codon usage bias has been extensively studied in metazoans, with both natural selection and mutation pressure playing important roles in different species. The disparate nature of metazoan codon usage patterns prevents the reconstruction of ancestral traits. However, traits conserved across holozoan protists highlight characteristics in the unicellular ancestors of Metazoa. Presented here are the patterns of codon usage in the choanoflagellates Monosiga brevicollis and Salpingoeca rosetta, as well as the filasterean Capsaspora owczarzaki. Codon usage is shown to be remarkably conserved. Highly biased genes preferentially use GC-ending codons, however there is limited evidence this is driven by local mutation pressure. The analyses presented provide strong evidence that natural selection, for both translational accuracy and efficiency, dominates codon usage bias in holozoan protists. In particular, the signature of selection for translational accuracy can be detected even in the most weakly biased genes. Biased codon usage is shown to have coevolved with the tRNA species, with optimal codons showing complementary binding to the highest copy number tRNA genes. Furthermore, tRNA modification is shown to be a common feature for amino acids with higher levels of degeneracy and highly biased genes show a strong preference for using modified tRNAs in translation. The translationally optimal codons defined here will be of benefit to future transgenics work in holozoan protists, as their use should maximise protein yields from edited transgenes.


Asunto(s)
Coanoflagelados/genética , Codón , Animales , Expresión Génica , Mutación , ARN de Transferencia/genética , Selección Genética
5.
Proc Natl Acad Sci U S A ; 113(19): 5358-63, 2016 May 10.
Artículo en Inglés | MEDLINE | ID: mdl-27118840

RESUMEN

Whereas all mammals have one glutamate dehydrogenase gene (GLUD1), humans and apes carry an additional gene (GLUD2), which encodes an enzyme with distinct biochemical properties. We inserted a bacterial artificial chromosome containing the human GLUD2 gene into mice and analyzed the resulting changes in the transcriptome and metabolome during postnatal brain development. Effects were most pronounced early postnatally, and predominantly genes involved in neuronal development were affected. Remarkably, the effects in the transgenic mice partially parallel the transcriptome and metabolome differences seen between humans and macaques analyzed. Notably, the introduction of GLUD2 did not affect glutamate levels in mice, consistent with observations in the primates. Instead, the metabolic effects of GLUD2 center on the tricarboxylic acid cycle, suggesting that GLUD2 affects carbon flux during early brain development, possibly supporting lipid biosynthesis.


Asunto(s)
Encéfalo/metabolismo , Ciclo del Ácido Cítrico/fisiología , Glutamato Deshidrogenasa/metabolismo , Ácido Glutámico/metabolismo , Metaboloma/fisiología , Transcriptoma/fisiología , Animales , Glutamato Deshidrogenasa/genética , Humanos , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Receptores de Glutamato/genética , Receptores de Glutamato/metabolismo , Proteínas Recombinantes/metabolismo , Especificidad de la Especie
6.
Glia ; 65(3): 474-488, 2017 03.
Artículo en Inglés | MEDLINE | ID: mdl-28032919

RESUMEN

A key enzyme in brain glutamate homeostasis is glutamate dehydrogenase (GDH) which links carbohydrate and amino acid metabolism mediating glutamate degradation to CO2 and expanding tricarboxylic acid (TCA) cycle capacity with intermediates, i.e. anaplerosis. Humans express two GDH isoforms, GDH1 and 2, whereas most other mammals express only GDH1. hGDH1 is widely expressed in human brain while hGDH2 is confined to astrocytes. The two isoforms display different enzymatic properties and the nature of these supports that hGDH2 expression in astrocytes potentially increases glutamate oxidation and supports the TCA cycle during energy-demanding processes such as high intensity glutamatergic signaling. However, little is known about how expression of hGDH2 affects the handling of glutamate and TCA cycle metabolism in astrocytes. Therefore, we cultured astrocytes from cerebral cortical tissue of hGDH2-expressing transgenic mice. We measured glutamate uptake and metabolism using [3 H]glutamate, while the effect on metabolic pathways of glutamate and glucose was evaluated by use of 13 C and 14 C substrates and analysis by mass spectrometry and determination of radioactively labeled metabolites including CO2 , respectively. We conclude that hGDH2 expression increases capacity for uptake and oxidative metabolism of glutamate, particularly during increased workload and aglycemia. Additionally, hGDH2 expression increased utilization of branched-chain amino acids (BCAA) during aglycemia and caused a general decrease in oxidative glucose metabolism. We speculate, that expression of hGDH2 allows astrocytes to spare glucose and utilize BCAAs during substrate shortages. These findings support the proposed role of hGDH2 in astrocytes as an important fail-safe during situations of intense glutamatergic activity. GLIA 2017;65:474-488.


Asunto(s)
Astrocitos/metabolismo , Ciclo del Ácido Cítrico/fisiología , Regulación Enzimológica de la Expresión Génica , Glucosa/deficiencia , Glutamato Deshidrogenasa/metabolismo , Ácido Glutámico/metabolismo , Animales , Astrocitos/efectos de los fármacos , Dióxido de Carbono/farmacocinética , Isótopos de Carbono/farmacocinética , Células Cultivadas , Corteza Cerebral/citología , Ciclo del Ácido Cítrico/efectos de los fármacos , Ciclo del Ácido Cítrico/genética , Relación Dosis-Respuesta a Droga , Proteína Ácida Fibrilar de la Glía/metabolismo , Glutamato Deshidrogenasa/genética , Ácido Glutámico/farmacología , Humanos , Ratones , Ratones Endogámicos C57BL , Ratones Transgénicos , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Deshidrogenasas del Alcohol de Azúcar/metabolismo , Tritio/farmacocinética
7.
BMC Genomics ; 18(1): 990, 2017 12 28.
Artículo en Inglés | MEDLINE | ID: mdl-29281970

RESUMEN

BACKGROUND: Synthetic systems that use positive feedback have been developed to control human disease vectors and crop pests. The tTAV system, which has been deployed in several insect species, relies on a positive feedback circuit that can be inhibited via dietary tetracycline. Although insects carrying tTAV fail to survive until adulthood in the absence of tetracycline, the exact reason for its lethality, as well as the transcriptomic effects of an active positive feedback circuit, remain unknown. RESULTS: We engineered the tTAV system in Drosophila melanogaster and investigated the effects of tTAV genome integration locus on the whole fly transcriptome during larval and adult life stages in four transgenic fly strains using gene expression microarrays. We found that while there were widespread effects on the transcriptome, the gene expression differences after removal of tetracycline were not consistent between integration sites. No specific region of the genome was affected, no common set of genes or pathways, nor did the integration site affect the transcripts in cis. CONCLUSION: Although the positive feedback tTAV system is effective at killing insect larvae regardless of where it is inserted in the genome, it does not exhibit a specific, consistent transcriptional signature. Instead, each insertion site is associated with broad, but different, transcriptional effects. Our results suggest that lethality may not be caused by a direct effect on transcription of a set of key genes or pathways. Instead, we propose that rather than a specific action of a tTAV protein, it is the stochastic transcriptional effects specific to each insertion site that contribute to the tTAV-induced mortality.


Asunto(s)
Drosophila melanogaster/genética , Regulación de la Expresión Génica , Genes Sintéticos , Transcripción Genética , Animales , Animales Modificados Genéticamente , Drosophila melanogaster/crecimiento & desarrollo , Drosophila melanogaster/metabolismo , Retroalimentación Fisiológica , Perfilación de la Expresión Génica , Análisis de Secuencia por Matrices de Oligonucleótidos , Especificidad de la Especie , Transcriptoma
8.
Proc Natl Acad Sci U S A ; 107(38): 16595-600, 2010 Sep 21.
Artículo en Inglés | MEDLINE | ID: mdl-20823249

RESUMEN

Mutations in ASPM (abnormal spindle-like microcephaly associated) cause primary microcephaly in humans, a disorder characterized by a major reduction in brain size in the apparent absence of nonneurological anomalies. The function of the Aspm protein in neural progenitor cell expansion, as well as its localization to the mitotic spindle and midbody, suggest that it regulates brain development by a cell division-related mechanism. Furthermore, evidence that positive selection affected ASPM during primate evolution has led to suggestions that such a function changed during primate evolution. Here, we report that in Aspm mutant mice, truncated Aspm proteins similar to those causing microcephaly in humans fail to localize to the midbody during M-phase and cause mild microcephaly. A human ASPM transgene rescues this phenotype but, interestingly, does not cause a gain of function. Strikingly, truncated Aspm proteins also cause a massive loss of germ cells, resulting in a severe reduction in testis and ovary size accompanied by reduced fertility. These germline effects, too, are fully rescued by the human ASPM transgene, indicating that ASPM is functionally similar in mice and humans. Our findings broaden the spectrum of phenotypic effects of ASPM mutations and raise the possibility that positive selection of ASPM during primate evolution reflects its function in the germline.


Asunto(s)
Microcefalia/genética , Mutación , Proteínas del Tejido Nervioso/genética , Animales , Animales Recién Nacidos , Secuencia de Bases , Encéfalo/anomalías , Proteínas de Unión a Calmodulina , Cartilla de ADN/genética , Modelos Animales de Enfermedad , Células Madre Embrionarias/patología , Femenino , Mutación de Línea Germinal , Humanos , Infertilidad/genética , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Mutantes , Ratones Transgénicos , Microcefalia/patología , Proteínas del Tejido Nervioso/fisiología , Neuronas/patología , Oligospermia/genética , Ovario/anomalías , Fragmentos de Péptidos/genética , Fragmentos de Péptidos/fisiología , Fenotipo , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Eliminación de Secuencia , Motilidad Espermática/genética , Testículo/anomalías
9.
Access Microbiol ; 5(9)2023.
Artículo en Inglés | MEDLINE | ID: mdl-37841098

RESUMEN

Synthetic biology enables the creative combination of engineering and molecular biology for exploration of fundamental aspects of biological phenomena. However, there are limited resources available for such applications in the educational context, where straightforward setup, easily measurable phenotypes and extensibility are of particular importance. We developed unigems, a set of ten plasmids that enable classroom-based investigation of gene-expression control and biological logic gates to facilitate teaching synthetic biology and genetic engineering. It is built on a high-copy plasmid backbone and is easily extensible thanks to a common primer set that facilitates Gibson assembly of PCR-generated or synthesized DNA parts into the target vector. It includes two reporter genes with either two constitutive (high- or low-level) or two inducible (lactose- or arabinose-) promoters, as well as a single-plasmid implementation of an AND logic gate. The set can readily be employed in undergraduate teaching settings, during outreach events and for training of iGEM teams. All plasmids have been deposited in Addgene.

10.
Mol Ecol Resour ; 22(8): 2860-2870, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-35668693

RESUMEN

Highly multiplexed approaches have become common in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals using combinatorially barcoded adapters. These strategies, however, can potentially misassigned reads to incorrect samples. Here, we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to 100 multiplexed samples per sequencing lane (639 samples in total). We created two types of sequencing libraries: four libraries of type A, where PCRs were run on individual samples before multiplexing, and three libraries of type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) than type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in type A and B libraries, respectively. We also show that increasing the number of mismatches allowed for barcode rescue to above 2 dramatically increases the number of recovered chimeric reads. We provide recommendations for developing highly multiplexed RAD-seq protocols and analysing the resulting data to minimize the generation of chimeric sequences, allowing their quantification and a finer control on the number of PCR cycles necessary to generate enough input DNA for library preparation.


Asunto(s)
ADN , Secuenciación de Nucleótidos de Alto Rendimiento , Quimera , Biblioteca de Genes , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Humanos , Análisis de Secuencia de ADN/métodos
11.
BMC Genomics ; 12: 91, 2011 Feb 01.
Artículo en Inglés | MEDLINE | ID: mdl-21284834

RESUMEN

BACKGROUND: Species with heteromorphic sex chromosomes face the challenge of large-scale imbalance in gene dose. Microarray-based studies in several independent male heterogametic XX/XY systems suggest that dosage compensation mechanisms are in place to mitigate the detrimental effects of gene dose differences. However, recent genomic research on female heterogametic ZZ/ZW systems has generated surprising results. In two bird species and one lepidopteran no evidence for a global dosage compensating mechanism has been found. The recent advent of massively parallel RNA sequencing now opens up the possibility to gauge the generality of this observation with a broader phylogenetic sampling. It further allows assessing the validity of microarray-based inference on dosage compensation with a novel technology. RESULTS: We here exemplify this approach using massively parallel sequencing on barcoded individuals of a bird species, the European crow (Corvus corone), where previously no genetic resources were available. Testing for Z-linkage with quantitative PCR (qPCR,) we first establish that orthology with distantly related species (chicken, zebra finch) can be used as a good predictor for chromosomal affiliation of a gene. We then use a digital measure of gene expression (RNA-seq) on brain transcriptome and confirm a global lack of dosage compensation on the Z chromosome. RNA-seq estimates of male-to-female (m:f) expression difference on the Z compare well to previous microarray-based estimates in birds and lepidopterans. The data further lends support that an up-regulation of female Z-linked genes conveys partial compensation and suggest a relationship between sex-bias and absolute expression level of a gene. Correlation of sex-biased gene expression on the Z chromosome across all three bird species further suggests that the degree of compensation has been partly conserved across 100 million years of avian evolution. CONCLUSIONS: This work demonstrates that the study of dosage compensation has become amenable to species where previously no genetic resources were available. Massively parallele transcriptome sequencing allows re-assessing the degree of dosage compensation with a novel tool in well-studies species and, in addition, gain valuable insights into the generality of mechanisms across independent taxonomic group for both the XX/XY and ZZ/ZW system.


Asunto(s)
Cuervos/genética , Cromosomas Sexuales/genética , Animales , Evolución Biológica , Compensación de Dosificación (Genética)/genética , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Masculino
12.
Insects ; 12(9)2021 Sep 18.
Artículo en Inglés | MEDLINE | ID: mdl-34564282

RESUMEN

Apis mellifera (honeybees) are a well-established model for the study of learning and cognition. A robust conditioning protocol, the olfactory conditioning of the proboscis extension response (PER), provides a powerful but straightforward method to examine the impact of varying stimuli on learning performance. Herein, we provide a protocol that leverages PER for classroom-based community or student engagement. Specifically, we detail how a class of high school students, as part of the Ryukyu Girls Outreach Program, examined the effects of caffeine and dopamine on learning performance in honeybees. Using a modified version of the PER conditioning protocol, they demonstrated that caffeine, but not dopamine, significantly reduced the number of trials required for a successful conditioning response. In addition to providing an engaging and educational scientific activity, it could be employed, with careful oversight, to garner considerable reliable data examining the effects of varying stimuli on honeybee learning.

13.
Nat Commun ; 12(1): 3898, 2021 06 23.
Artículo en Inglés | MEDLINE | ID: mdl-34162854

RESUMEN

One topical area of supramolecular chemistry is the binding of anionic species but despite the importance of anions in diverse cellular processes and for cancer development, anion receptors or 'binders' have received little attention as potential anti-cancer therapeutics. Here we report self-assembling trimetallic cryptands (e.g. [L2(Metal)3]6+ where Metal = Cu2+, Zn2+ or Mn2+) which can encapsulate a range of anions and which show metal-dependent differences in chemical and biological reactivities. In cell studies, both [L2Cu3]6+ and [L2Zn3]6+ complexes are highly toxic to a range of human cancer cell lines and they show significant metal-dependent selective activity towards cancer cells compared to healthy, non-cancerous cells (by up to 2000-fold). The addition of different anions to the complexes (e.g. PO43-, SO42- or PhOPO32-) further alters activity and selectivity allowing the activity to be modulated via a self-assembly process. The activity is attributed to the ability to either bind or hydrolyse phosphate esters and mechanistic studies show differential and selective inhibition of multiple kinases by both [L2Cu3]6+ and [L2Zn3]6+ complexes but via different mechanisms.


Asunto(s)
Aniones/química , Antineoplásicos/química , Complejos de Coordinación/química , Metales/química , Células A549 , Antineoplásicos/farmacología , Autofagia/efectos de los fármacos , Western Blotting , Línea Celular , Línea Celular Tumoral , Supervivencia Celular/efectos de los fármacos , Complejos de Coordinación/farmacología , Cristalografía por Rayos X , Células HCT116 , Células HT29 , Humanos , Concentración 50 Inhibidora , Neoplasias/metabolismo , Neoplasias/patología , Fosfotransferasas/antagonistas & inhibidores , Fosfotransferasas/metabolismo
14.
Sci Rep ; 11(1): 18121, 2021 09 13.
Artículo en Inglés | MEDLINE | ID: mdl-34518562

RESUMEN

Historical records document medieval immigration from North Africa to Iberia to create Islamic al-Andalus. Here, we present a low-coverage genome of an eleventh century CE man buried in an Islamic necropolis in Segorbe, near Valencia, Spain. Uniparental lineages indicate North African ancestry, but at the autosomal level he displays a mosaic of North African and European-like ancestries, distinct from any present-day population. Altogether, the genome-wide evidence, stable isotope results and the age of the burial indicate that his ancestry was ultimately a result of admixture between recently arrived Amazigh people (Berbers) and the population inhabiting the Peninsula prior to the Islamic conquest. We detect differences between our sample and a previously published group of contemporary individuals from Valencia, exemplifying how detailed, small-scale aDNA studies can illuminate fine-grained regional and temporal differences. His genome demonstrates how ancient DNA studies can capture portraits of past genetic variation that have been erased by later demographic shifts-in this case, most likely the seventeenth century CE expulsion of formerly Islamic communities as tolerance dissipated following the Reconquista by the Catholic kingdoms of the north.


Asunto(s)
Dieta , Genética de Población , Migración Humana , África del Norte , Antropología , Arqueología , Antecedentes Genéticos , Genoma Humano , Historia Medieval , Humanos , Filogenia , Filogeografía , España
15.
Oncol Rep ; 16(5): 1041-5, 2006 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-17016590

RESUMEN

Somatic mitochondrial DNA (mtDNA) mutations have been found in a subset of endometrial cancers (EC) from different populations. We have investigated the relationship between mtDNA changes and clinical and pathological variables of women affected by EC. mtDNA mutations were detected both in early (3/32; 9%) and in advanced (1/8; 12%) stages of uterine tumors. However, patients carrying the mtDNA mutations or the normal mtDNA sequence had indistinguishable clinicopathological data, including age, clinical stage, histological grade and type or depth of myometrial invasion. It is noteworthy that mtDNA mutations were not detected in hyperplastic endometrial tissues or in ECs coexisting with hyperplasia, nor in a single case of endometrial stromal sarcoma. LOH at the tumor suppressor genes RB1 and TP53 as well as p16INK4A alterations (LOH, gene deletion) were found in tumors carrying mtDNA mutations. These results suggest that somatic mtDNA mutations are detected in a subset of ECs, although they are unrelated to clinicopathological variables of cancer.


Asunto(s)
ADN Mitocondrial/genética , Neoplasias Endometriales/genética , Neoplasias Endometriales/patología , Mutación , Adulto , Anciano , Anciano de 80 o más Años , ADN de Neoplasias/genética , Supervivencia sin Enfermedad , Hiperplasia Endometrial/genética , Hiperplasia Endometrial/patología , Hiperplasia Endometrial/cirugía , Neoplasias Endometriales/cirugía , Femenino , Humanos , Pérdida de Heterocigocidad , Persona de Mediana Edad , Sarcoma Estromático Endometrial/genética , Sarcoma Estromático Endometrial/patología , Sarcoma Estromático Endometrial/cirugía
16.
Mitochondrion ; 3(2): 119-24, 2003 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-16120350

RESUMEN

We have analyzed mtDNA variation in various cancer samples, comparing them with normal tissue controls, and identified mutations and polymorphisms, both known and novel, in mitochondrial tRNA, rRNA and protein genes. Most remarkably, in a colon cancer sample we have found the A3243G mutation in the homoplasmic state. This mutation is known to cause severe mitochondrial dysfunction and, until now, has not been found in cancer cells, nor in the homoplasmic state in living subjects. The mutation was absent from normal tissue, suggesting that mtDNA mutation and resulting respiratory deficiency played a role in carcinogenesis.

17.
Toxicol Mech Methods ; 14(1-2): 85-90, 2004.
Artículo en Inglés | MEDLINE | ID: mdl-20021129

RESUMEN

Mitochondria, cellular powerhouses, play a central role in apoptosis. In addition, they are suspected to contribute to aging. There is also increasing evidence that abnormalities in mitochondrial function help cancer development. Changes in mitochondrial transcription and oxidative phosphorylation pathways are observed in many types of cancer. Somatic mutations and quantitative changes in mitochondrial DNA were found in tumors, suggesting that alterations in mitochondrial DNA and the resulting respiratory deficiency play a role in carcinogenesis. It was postulated they could be useful as cancer markers. Mitochondria with abnormal functions are suitable targets for anticancer drugs.

18.
Front Genet ; 5: 153, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24917877

RESUMEN

Copy-number variants (CNVs) may play an important role in early adaptations, potentially facilitating rapid divergence of populations. We describe an approach to study this question by investigating CNVs present in natural populations of mice in the early stages of divergence and their involvement in selective sweeps. We have analyzed individuals from two recently diverged natural populations of the house mouse (Mus musculus domesticus) from Germany and France using custom, high-density, comparative genome hybridization arrays (CGH) that covered almost 164 Mb and 2444 genes. One thousand eight hundred and sixty one of those genes we previously identified as differentially expressed between these populations, while the expression of the remaining genes was invariant. In total, we identified 1868 CNVs across all 10 samples, 200 bp to 600 kb in size and affecting 424 genic regions. Roughly two thirds of all CNVs found were deletions. We found no enrichment of CNVs among the differentially expressed genes between the populations compared to the invariant ones, nor any meaningful correlation between CNVs and gene expression changes. Among the CNV genes, we found cellular component gene ontology categories of the synapse overrepresented among all the 2444 genes tested. To investigate potential adaptive significance of the CNV regions, we selected six that showed large differences in frequency of CNVs between the two populations and analyzed variation in at least two microsatellites surrounding the loci in a sample of 46 unrelated animals from the same populations collected in field trappings. We identified two loci with large differences in microsatellite heterozygosity (Sfi1 and Glo1/Dnahc8 regions) and one locus with low variation across the populations (Cmah), thus suggesting that these genomic regions might have recently undergone selective sweeps. Interestingly, the Glo1 CNV has previously been implicated in anxiety-like behavior in mice, suggesting a differential evolution of a behavioral trait.

19.
PLoS One ; 9(3): e91295, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24618910

RESUMEN

BACKGROUND: Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. RESULTS: Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. CONCLUSION: The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations.


Asunto(s)
Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Análisis de Secuencia por Matrices de Oligonucleótidos/normas , Animales , Calibración , Variaciones en el Número de Copia de ADN , Perfilación de la Expresión Génica , Ratones , Reproducibilidad de los Resultados
20.
PLoS One ; 9(5): e97557, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24844466

RESUMEN

The idea of introducing genetic modifications into wild populations of insects to stop them from spreading diseases is more than 40 years old. Synthetic disease refractory genes have been successfully generated for mosquito vectors of dengue fever and human malaria. Equally important is the development of population transformation systems to drive and maintain disease refractory genes at high frequency in populations. We demonstrate an underdominant population transformation system in Drosophila melanogaster that has the property of being both spatially self-limiting and reversible to the original genetic state. Both population transformation and its reversal can be largely achieved within as few as 5 generations. The described genetic construct {Ud} is composed of two genes; (1) a UAS-RpL14.dsRNA targeting RNAi to a haploinsufficient gene RpL14 and (2) an RNAi insensitive RpL14 rescue. In this proof-of-principle system the UAS-RpL14.dsRNA knock-down gene is placed under the control of an Actin5c-GAL4 driver located on a different chromosome to the {Ud} insert. This configuration would not be effective in wild populations without incorporating the Actin5c-GAL4 driver as part of the {Ud} construct (or replacing the UAS promoter with an appropriate direct promoter). It is however anticipated that the approach that underlies this underdominant system could potentially be applied to a number of species.


Asunto(s)
Cromosomas de Insectos/genética , Genética de Población/métodos , Transformación Genética , Animales , Drosophila melanogaster , Técnicas de Silenciamiento del Gen/métodos , Humanos
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