Farmer (From the Imagination of Darren Page)

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This will benefit both IVF patients and prospective parents at risk of aneuploid offspring following natural conception. The production of pig preimplantation embryos in vitro: Current progress and future prospects. Reproductive Biology [Online] 18 Human assisted reproductive technology procedures are routinely performed in clinics globally, and some of these approaches are now common in other mammals such as cattle.

This is currently not the case in pigs. Given that the global population is expected to increase by over two billion people between now and , the demand for meat will also undoubtedly increase. With this in mind, a more sustainable way to produce livestock; increasing productivity and implementing methods that will lead to faster genetic selection, is imperative.

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The establishment of routine and production scale pig embryo in vitro production could be a solution to this problem. Producers would be able to increase the overall number of offspring born, animal transportation would be more straightforward and in vitro produced embryos could be produced from the gametes of selected elite.

Here we review the most recent developments in pig embryology, outline the current barriers and key challenges that exist, and outline research priorities to surmount these difficulties. Joseph, S. Diversity [Online] 10 Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly.

Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made.

The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome.

Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Standard ideograms that are generated here helped to map predicted chromosomal fragments PCFs from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons.

Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly.

Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes.

Such assemblies are essential for studies of genotype-to-phenotype association, gross genomic evolution, and speciation. Inter-species differences can arise from chromosomal changes fixed during evolution, and we previously hypothesized that a higher fraction of elements under negative selection contributed to avian-specific phenotypes and avian genome organization stability. The objective of this study is to generate chromosome-level assemblies of three avian species saker falcon, budgerigar, and ostrich previously reported as karyotypically rearranged compared to most birds.

We also test the hypothesis that the density of conserved non-coding elements is associated with the positions of evolutionary breakpoint regions. Results: We used reference-assisted chromosome assembly, PCR, and lab-based molecular approaches, to generate chromosome-level assemblies of the three species.

We mapped inter- and intrachromosomal changes from the avian ancestor, finding no interchromosomal rearrangements in the ostrich genome, despite it being previously described as chromosomally rearranged. We found that the average density of conserved non-coding elements in evolutionary breakpoint regions is significantly reduced. Fission evolutionary breakpoint regions have the lowest conserved non-coding element density, and intrachromomosomal evolutionary breakpoint regions have the highest.

Moreover, conserved non-coding elements are important factors in defining where rearrangements, especially interchromosomal, are fixed during evolution without deleterious effects. Singchat, W. BMC Genomics [Online] To investigate the process of sex chromosome differentiation and evolution between cobras, most snakes, and other amniotes, we constructed a chromosome map of the Siamese cobra Naja kaouthia with 43 bacterial artificial chromosomes BACs derived from the chicken and zebra finch libraries using the fluorescence in situ hybridization FISH technique, and compared it with those of the chicken, the zebra finch, and other amniotes.

Results We produced a detailed chromosome map of the Siamese cobra genome, focusing on chromosome 2 and sex chromosomes. Interestingly, twelve BACs that had partial homology with sex chromosomes of several amniotes were mapped on the heterochromatic NKAW as hybridization signals such as repeat sequences. Sequence analysis showed that most of these BACs contained high proportions of transposable elements. Conclusions The frequent amplification of repeats might involve heterochromatinization and promote sex chromosome differentiation in the Siamese cobra W sex chromosome.

Repeat sequences are also shared among amniote sex chromosomes, which supports the hypothesis of an ancestral super-sex chromosome with overlaps of partial syntenies. Alternatively, amplification of microsatellite repeat motifs could have occurred independently in each lineage, representing convergent sex chromosomal differentiation among amniote sex chromosomes.

Patterns of microchromosome organization remain highly conserved throughout avian evolution. Chromosoma [Online]. The structure and organization of a species genome at a karyotypic level, and in interphase nuclei, have broad functional significance. Although regular sized chromosomes are studied extensively in this regard, microchromosomes, which are present in many terrestrial vertebrates, remain poorly explored. In species where microchromosomes have fused to other chromosomes, they retain genomic features such as gene density and GC content; however, the extent to which they retain a central nuclear position has not been investigated.

In studying 22 avian species from 10 orders, we established that, other than in species where microchromosomal fusion is obvious Falconiformes and Psittaciformes , there was no evidence of microchromosomal rearrangement, suggesting an evolutionarily stable avian genome karyotypic organization. Moreover, in species where microchromosomal fusion has occurred, they retain a central nuclear location, suggesting that the nuclear position of microchromosomes is a function of their genomic features rather than their physical size.

Chromosoma [Online] Saintas, E. The formation of acquired drug resistance is a major reason for the failure of anti-cancer therapies after initial response. Notably, UVC-induced DNA damage is thought to be predominantly repaired by nucleotide excision repair and nucleotide excision repair has been described as the main oxaliplatin-induced DNA damage repair system. In conclusion, we introduce a novel oxaliplatin resistance model. Models of oxaliplatin resistance are of particular relevance since research on platinum drugs has so far predominantly focused on cisplatin and carboplatin.

Volume 420 Issue 6915, 5 December 2002

Continuing to deliver: the evidence base for pre-implantation genetic screening. BMJ [Online] :j View in KAR View full text. Sanders, K. Journal of Fetal Medicine [Online] 4 Preimplantation genetic diagnosis PGD , first successfully carried out in humans in the early s, initially involved the PCR sexing of embryos by Y- and later also X- chromosome specific detection. Because of the problems relating to misdiagnosis and contamination of this technology however the PCR based test was superseded by a FISH-based approach involving X and Y specific probes. Aneuploidy is widely accepted to be the leading cause of implantation failure in assisted reproductive technology ART and a major contributor to miscarriage, especially in women of advanced maternal age.

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The current practice of trophectoderm biopsy followed by array CGH or next generation sequencing is gaining in popularity however as evidence for its efficacy grows. PGS has the potential to identify viable embryos that can be transferred thereby reducing the chances of traumatic failed IVF cycles, miscarriage or congenital abnormalities and facilitating the quickest time to live birth of chromosomally normal offspring. In parallel to chromosomal diagnoses, technology for PGD has allowed for improvements in accuracy and efficiency of the genetic screening of embryos for monogenic disorders.

The number of genetic conditions available for screening has increased since the early days of PGD, with the human fertilization and embryology authority currently licensing conditions in the UK [1]. A novel technique known as karyomapping that involves SNP chip screening and tracing inherited chromosomal haploblocks is now licensed for the PGD detection of monogenic disorders.

Its potential for the universal detection of chromosomal and monogenic disorders simultaneously however, has yet to be realized. Gould, R. Karyomapping and how is it improving preimplantation genetics?. Expert Review of Molecular Diagnostics [Online]. Areas Covered: The area of preimplantation genetics has evolved over the last 25 years, adapting to changes in technology and the need for more efficient, streamlined diagnoses. Karyomapping allows the determination of inheritance from the grand parental haplobocks through assembly of inherited chromosomal segments.

The output displays homologous chromosomes, crossovers and the genetic status of the embryos by linkage comparison, as well as chromosomal disorders. It also allows for determination of heterozygous SNP calls, avoiding the risks of allele dropout, a common problem with other PGD techniques. Manuscripts documenting the evolution of preimplantation genetics, especially those investigating technologies that would simultaneously detect monogenic and chromosomal disorders, were selected for review.

Due an inability to detect post-zygotic trisomy reliably however and confounding problems of embryo mosaicism, karyomapping has yet to be applied clinically for detection of chromosome disorders. Isolation of subtelomeric sequences of porcine chromosomes for translocation screening reveals errors in the pig genome assembly. Animal Genetics [Online] 48 Balanced chromosomal aberrations have been shown to affect fertility in most species studied, often leading to hypoprolificacy reduced litter size in domestic animals such as pigs.

With an increasing emphasis in modern food production on the use of a small population of high quality males for artificial insemination, the potential economic and environmental costs of hypoprolific boars, bulls, rams etc.

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There is therefore a need for novel tools to facilitate rapid, cost-effective chromosome translocation screening. This has previously been achieved by standard karyotype analysis; however, this approach relies on a significant level of expertise and is limited in its ability to identify subtle, cryptic translocations. To address this problem, we developed a novel device and protocol for translocation screening using subtelomeric probes and fluorescence in situ hybridisation.

Probes were designed using BACs bacterial artificial chromosomes from the subtelomeric region of the short p-arm and long q-arm of each porcine chromosome. Initial experiments designed to isolate BACs in subtelomeric regions led to the discovery of a series of incorrectly mapped regions in the porcine genome assembly from a total of 82 BACs, only 45 BACs mapped correctly. Our work therefore highlights the importance of accurate physical mapping of newly sequenced genomes. The system herein described allows for robust and comprehensive analysis of the porcine karyotype, an adjunct to classical cytogenetics that provides a valuable tool to expedite efficient, cost effective food production.

Saretzki, G. Preterm infants have significantly longer telomeres than their term born counterparts. There are well-established morbidities associated with preterm birth including respiratory, neurocognitive and developmental disorders. These include hypertension, insulin resistance and altered body fat distribution. Evidence shows that these morbidities persist into adult life, posing a significant public health concern. In this study, we measured relative telomere length in leukocytes as an indicator of biological ageing in 25 preterm infants at term equivalent age.

Comparing our measurements with those from 22 preterm infants sampled at birth and from 31 term-born infants, we tested the hypothesis that by term equivalent age, preterm infants have significantly shorter telomeres thus suggesting that they are prematurely aged. Our results demonstrate that relative telomere length is highly variable in newborn infants and is significantly negatively correlated with gestational age and birth weight in preterm infants. Contrary to our initial hypothesis however, relative telomere length was significantly shortest in the term born control group compared to both preterm groups and longest in the preterm at birth group.

In addition, telomere lengths were not significantly different between preterm infants sampled at birth and those sampled at term equivalent age. These results indicate that other, as yet undetermined, factors may influence telomere length in the preterm born infant and raise the intriguing hypothesis that as preterm gestation declines, telomere attrition rate increases. What is Karyomapping and where does it fit in the world of preimplantation genetic diagnosis PGD?.

Medical Research Archives [Online] 5. The first application of preimplantation genetic diagnosis PGD recently celebrated its 25th birthday. Aside from the very early days when chromosomal diagnoses were used by sexing for the selective implantation of embryos unaffected by sex linked disorders, the paths of chromosomal and monogenic PGD have diverged. For monogenic disorders, progress has been impeded by the need to tailor each diagnosis to the mutation in question. Karyomapping is a novel approach that allows the detection of the inheritance of grand parental haploblocks through the identification of inherited chromosomal segments.

It involves genome-wide single nucleotide polymorphism SNP analysis of parental DNA, a reference from a related individual of known disease status typically an affected child and amplified DNA form biopsied cells of the usually lastocyst embryos in question. Identification of informative loci for each of four parental haplotypes is followed by direct comparison to the reference, ultimately creating a Karyomap.

The Karyomapping programme Illumina displays homologous chromosomes, points of crossing over and the haplotype of each of the embryos. It also detects meiotic trisomy, monosomy, triploidy and uniparental heterodisomy some of which NGS and aCGH will not. Karyomapping is currently in use for the detection of monogenic disorders and around clinics offer it worldwide making use of about 20 diagnostic laboratories. At the time of writing, over two and a half thousand clinical cases have been performed.

Because of the limited detection of some post-zygotic errors such as post-zygotic trisomy which can also lead to mosaicism, Karyomapping has not yet been fully applied clinically for aneuploidy screening. The diagnostic potential of the technique will be fully recognised with the application of this technology on clinical cases. McCallie, B. Infertility diagnosis has a significant impact on the transcriptome of developing blastocysts. Molecular Human Reproduction [Online] 23 Limited information is known regarding the relationship between a specific infertility diagnosis and blastocyst transcription during preimplantation development.

Functional annotation of biological and molecular processes revealed both similarities, as well as differences, across the infertility groups. All infertility etiologies displayed transcriptome alterations in signal transducer activity, receptor binding, reproduction, cell adhesion and response to stimulus. Blastocysts from PCO patients were also enriched for apoptotic genes while MF blastocysts displayed enrichment for genes involved in cancer processes.

Blastocysts from couples with unexplained infertility displayed transcription alterations related to various disease states, which included mechanistic target of rapamycin mTOR and adipocytokine signaling. Caujolle, S. Speckle variance OCT for depth resolved assessment of the viability of bovine embryos. Biomedical Optics Express [Online] 8 The morphology of embryos produced by in vitro fertilization IVF is commonly used to estimate their viability.

However, imaging by standard microscopy is subjective and unable to assess the embryo on a cellular scale after compaction. Optical coherence tomography is an imaging technique that can produce a depth-resolved profile of a sample and can be coupled with speckle variance SV to detect motion on a micron scale. In this study, day 7 post-IVF bovine embryos were observed either short-term 10 minutes or longterm over 18 hours and analyzed by swept source OCT and SV to resolve their depth profile and characterize micron-scale movements potentially associated with viability.

The percentage of en face images showing movement at any given time was calculated as a method to detect the vital status of the embryo. This method could be used to measure the levels of damage sustained by an embryo, for example after cryopreservation, in a rapid and non-invasive way. Ioannou, D.

Impact of sperm DNA chromatin in the clinic. Journal of Assisted Reproduction and Genetics [Online] 33 View in KAR.

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Upgrading molecular cytogenetics to study reproduction and reproductive isolation in mammals, birds, and dinosaurs. The past 10—15 years have seen a revolution in the field of genomics, first with the human genome project, followed by those of key model and agricultural species chicken, pig, cattle, sheep and, most recently,? Chromosome rearrangements are biologically relevant both in the context of reduction in reproductive capability of individual animals and in the establishment in reproductive isolation as species evolve and diverge.

Moreover, a karyotype effectively represents a low-resolution map of the genome of any species. In investigating all these aspects, FISH remains the tool of choice, and this study describes a step change in its use. Capalbo, A. Artificial oocyte activation with calcium ionophore does not cause a widespread increase in chromosome segregation errors in the second meiotic division of the oocyte. Objective To study the effect of artificial oocyte activation AOA on chromosome segregation errors in the meiotic divisions.

Design Prospective cohort study with historical control. Intervention s Oocytes were activated by 40 minutes' exposure to ? M calcium-ionophore. A control sample of embryos derived from normally fertilized oocytes was included for comparison. Main Outcome Measure s Incidence of chromosome segregation errors in artificially activated and normally fertilized oocytes in relation to pronuclear evaluation. Result s Of 49 oocytes that survived the warming procedure, thirty-nine Most activated normally, resulting in extrusion of the second polar body and formation of a single or no pronucleus 2PB1PN: 30 of 39, Twenty-seven of these were analyzed, and 16 Single-nucleotide polymorphism analysis of normally activated oocytes confirmed normal segregation of maternal chromosomes.

No difference in the proportion of meiosis II type errors was observed between artificially activated oocytes The abnormally activated oocytes, with? Conclusion s From this preliminary dataset, there is no evidence that AOA causes a widespread increase in chromosome segregation errors in meiosis II.

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However, we recommend that it be applied selectively to patients with specific indications. Corona cell RNA sequencing from individual oocytes revealed transcripts and pathways linked to euploid oocyte competence and live birth. Reproductive BioMedicine Online [Online] 32 Corona cells surround the oocyte and maintain a close relationship through transzonal processes and gap junctions, and may be used to assess oocyte competence.

In this study, the corona cell transcriptome of individual cumulus oocyte complexes COCs was investigated. Isolated corona cells were collected from COCs that developed into euploid blastocysts and were transferred in a subsequent frozen embryo transfer. Ten corona cell samples underwent RNA-sequencing to generate unique gene expression profiles. Live birth was compared with negative implantation after the transfer of a euploid blastocyst using bioinformatics and statistical analysis.

Individual corona cell samples produced a mean of Enriched pathway analysis showed Wnt signalling, mitogen-activated protein kinases signalling, focal adhesion and tricarboxylic acid cycle to be affected by implantation outcome. Individual, corona cell transcriptome was successfully generated using RNA-sequencing. Key genes and signalling pathways were identified in association with implantation outcome after the transfer of a euploid blastocyst in a frozen embryo transfer. These data could provide novel biomarkers for the non-invasive assessment of embryo viability.

Multicolor detection of every chromosome as a means of detecting mosaicism and nuclear organization in human embryonic nuclei. Panminerva medica [Online] 58 Fluorescence in-situ hybridization FISH revolutionized cytogenetics using fluorescently labelled probes with high affinity with target nuclear DNA.

By the early s FISH was adopted as a means of preimplantation genetic diagnosis PGD sexing for couples at risk of transmitting X-linked disorders and later for detection of unbalanced translocations. Following a rise in popularity of PGD by FISH for sexing and the availability of multicolor probes colors , the use of FISH was expanded to the detection of aneuploidy and selective implantation of embryos more likely to be euploid, the rationale being to increase pregnancy rates referral categories were typically advanced maternal age, repeated IVF failure, repeated miscarriage or severe male factor infertility.

Despite initial reports of an increase in implantation rates, reduction in trisomic offspring and spontaneous abortions criticism centered around experimental design including lack of randomization , inadequate control groups and lack of report on live births.

Cell-by-cell follow up analysis of individual blastomeres in non-transferred embryos is however usually prohibitively expensive by these new approaches and thus FISH remains an invaluable resource for the study of mosaicism and nuclear organization. We thus developed the approach described herein for the FISH detection of chromosome copy number of all 24 human chromosomes. This approach involves 4 sequential layers of hybridization, each with 6 spectrally distinct fluorochromes and a bespoke capturing system. Here we report previously published studies and hitherto unreported data indicating that 24 chromosome FISH is a useful tool for studying chromosome mosaicism, one of the most hotly debated topics currently in preimplantation genetics.

Our results suggest that mosaic embryo aneuploidy is not highly significantly correlated to maternal age, probably due, in part, to the large preponderance of post-zygotic mitotic errors. Chromosome loss anaphase lag appears to be the most common mechanism, followed by chromosome gain endoreduplication , however mitotic non-disjunction of chromosomes appears to be rare.

Nuclear organization i. By the blastocyst stage however, a more ordered organization with spatial and temporal cues important for embryo development appears. We have however found no association between aneuploidy and nuclear organization using this approach despite our earlier studies. In conclusion, while FISH is mostly "dead and buried" for mainstream PGS, it still has a place for basic biology studies; the development of a 24 chromosome protocol extends the power of this analysis.

Al Dibouni, Z. To determine if prolonged time in embryo culture has an effect on the rate, sex ratio, and perinatal outcomes of monozygotic twins MZT following either cleavage stage or blastocyst embryo transfer after assisted conception. This is a retrospective study of 2, consecutive clinical pregnancies resulting from cleavage stage transfer CT and blastocyst transfer BT.

Criteria examined included i incidences ii sex ratios iii gestational age and birth weight; iv perinatal outcomes of these pregnancies from cleavage stage and blastocyst transfer procedures. Monozygotic twin pregnancies were identified by i presence of a gestational sac containing more than one fetal pole with cardiac activity, ii the number of gestational sacs or fetal hearts exceeds the number of embryos transferred and iii twin pregnancies following a single embryo transfer.

Overall the incidence of twinning was 1. The frequency of twinning was 2. There was no statistically significant difference between transfer type and gestational age, birth weight and perinatal outcome. All pregnancies resulted in the birth of 86 infants. In our experience, BT more than doubles the chances of conceiving a monozygotic twin pregnancy, however IVF techniques lead to a greater likelihood of male birth s if twins are conceived.

Appropriate pre-conception counselling should be given to advise the potential risks associated with both types of transfer as well as using alternative methods such as single embryo transfer to reduce the risk of multiple gestations. Wrenzycki, C. DNA methylation is a key epigenetic mechanism responsible for gene regulation, chromatin remodeling, and genome stability, playing a fundamental role during embryonic development.

The aim of this study was to determine if these epigenetic marks are associated with chromosomal aneuploidy in human blastocysts. Surplus, cryopreserved blastocysts that were donated to research with IRB consent were chosen with varying chromosomal aneuploidies and respective implantation potential: monosomies and trisomies 7, 11, 15, 21, and The methylation profiles of these human blastocysts were found to be similar across all samples, independent of chromosome constitution; however, more detailed examination identified significant hypomethylation in the chromosome involved in the monosomy.

In summary, monosomy blastocysts displayed hypomethylation for the chromosome involved in the error, as well as transcription alterations of associated developmental genes. Together, these modifications may be contributing to genetic instability and therefore be responsible for the limited implantation potential observed for full monosomy blastocysts. Coates, A. Differences in pregnancy outcomes in donor egg frozen embryo transfer FET cycles following preimplantation genetic screening PGS : a single center retrospective study.

Journal of Assisted Reproduction and Genetics [Online] 34 Genome Biology and Evolution [Online] 8 Homologous synteny blocks HSBs and evolutionary breakpoint regions EBRs in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm.

Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes.

Taylor, T. Cytogenetic and Genome Research [Online] The purpose of this study was to identify a technique that allows for comprehensive chromosome screening CCS of individual cells within human blastocysts along with the approximation of their location in the trophectoderm relative to the inner cell mass ICM.

This proof-of-concept study will allow for a greater understanding of chromosomal mosaicism at the blastocyst stage and the mechanisms by which mosaicism arises. One blastocyst was held by a holding pipette and the ICM was removed. While still being held, the blastocyst was further biopsied into quadrants. A holding pipette was used to aspirate the sections until individual cells were isolated.

A total of 18 cells were used for analysis, of which 15 Fifteen cells were isolated from the trophectoderm; 13 Twelve cells were euploid 46,XY , while 1 was complex abnormal 44,XY , presenting with monosomy 7, 10, 11, 13, and 19, and trisomy 14, 15, and Here, we expand on a previously published technique which disassociates biopsied sections of the blastocyst into individual cells. Since the blastocyst sections were biopsied in regard to the position of the ICM, it was possible to reconstruct a virtual image of the blastocyst while presenting each cell's individual CCS results.

Accurate quantitation of mitochondrial DNA reveals uniform levels in human blastocysts irrespective of ploidy, age, or implantation potential. Hornak, M. Bovine embryos are now routinely used in agricultural systems as a means of disseminating superior genetics worldwide, ultimately with the aim of feeding an ever-growing population. Further investigations, common for human IVF embryos, thus have priority to improve cattle IVF, as has screening for aneuploidy abnormal chromosome number. Although the incidence and consequences of aneuploidy are well documented in human preimplantation embryos, they are less well known for the embryos of other animals.

To address this, we assessed aneuploidy levels in thirty-one 2-cell bovine embryos derived from early- and late-cleaving zygotes. Contemporary approaches Whole Genome Amplification and next-generation sequencing allowed aneuploidy assessment for all chromosomes in oocytes from donors aged years. We also quantified mitochondrial DNA mtDNA levels in all blastomeres assessed, thereby testing the hypothesis that they are related to levels of aneuploidy.

The overall incidence of aneuploidy in this cohort of bovine embryos was Moreover, based on mtDNA sequence read counts, we observed that the median mtDNA quantity is significantly lower in late-cleaving embryos. These findings further reinforce the use of the bovine system as a model for human IVF studies. Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research [Online] 27 Most recent initiatives to sequence and assemble new species' genomes de-novo fail to achieve the ultimate endpoint to produce contigs, each representing one whole chromosome.

Even the best-assembled genomes using contemporary technologies consist of sub-chromosomal sized scaffolds. To circumvent this problem, we developed a novel approach that combines computational algorithms to merge scaffolds into chromosomal fragments, PCR-based scaffold verification and physical mapping to chromosomes.

Multi-genome-alignment-guided probe selection led to the development of a set of universal avian BAC clones that permit rapid anchoring of multiple scaffolds to chromosomes on all avian genomes. As proof of principle, we assembled genomes of the pigeon Columbia livia and peregrine falcon Falco peregrinus to chromosome level comparable, in continuity, to avian reference genomes. Using chromosome breakpoint data, we established that avian interchromosomal breakpoints appear in the regions of low density of conserved non-coding elements CNEs and that the chromosomal fission sites are further limited to long CNE 'deserts.

High-throughput multiple hybridization and rapid capture strategies using the current BAC set provide the basis for assembling numerous avian and possibly other reptilian species while the overall strategy for scaffold assembly and mapping provides the basis for an approach that provided metaphases can be generated could be applied to any animal genome.

Gross genome evolution in the Dinosauria Griffin, D. The Dinosaurs dominated the terrestrial environment for around million years and are probably the most successful land vertebrate group to have existed. They survived several mass extinction events before finally all non-avian species were wiped out 66 million years ago in the Cretaceous-Paleogene extinction event. The neornithes modern birds are their living descendants. Despite the huge phenotypic diversity seen in birds, they, and some non-avian reptiles e.

Donegal may initially appear to be unlikely farmers. The duo, based in Gurteen, Carrigallen, Co. That is where I spent a very happy childhood and my love for the independence of the faming lifestyle grew. The different personalities of each dairy cow made me realise that cows deserved to be treated ethically. Following the celebration of his 13 th birthday, the family no longer continued dairy farming and Darren later went the other side of the farm gate to complete his Archaeology degree at I.

During the degree programme, Darren met Rose his partner and they decided to establish a small holding in , due to their experience in the livestock and horticultural disciplines. We got our herd number and the rest is now history. Due to the nature of their profession as archaeologists keen to preserve and investigate all parts of our history, it is no wonder that Darren and his partner Rose have turned their attention to two rather unique cattle breeds.

The duo crossed paths with the famous conservationist and rare breeder Mr. Noel Kiernan which stands out as a major milestone. Keirnan encouraged Darren to join the Irish Droimeann Cattle Society and his interest in rare breeds continued to snowball. As both cattle breeds are not to be found in their numbers in Ireland, sourcing the foundational females of the herd became a rather difficult journey for the rare cattle breeds enthusiast.