Additional Genetic Material Research Articles

Genomic Balancing Act: deciphering DNA rearrangements in the complex chromosomal aberration involving 5p15.2, 2q31.1, and 18q21.32.

Despite extensive research into the genetic underpinnings of neurodevelopmental disorders (NDD), many clinical cases remain unresolved. We studied a female proband with a NDD, mildly dysmorphic facial features, and brain stem hypoplasia on neuroimaging. Comprehensive genomic analyses revealed a terminal 5p loss and aterminal 18q gain in the proband while a diploid copy number for chromosomes 5 and 18 in both parents. Genomic investigations in the proband identified an unbalanced translocation t(5;18) with additional genetic material from chromosome 2 (2q31.3) inserted at the breakpoint, pointing to a complex chromosomal rearrangement (CCR) involving 5p15.2, 2q31.3, and 18q21.32. Breakpoint junction analyses enabled by long-read genome sequencing unveiled the presence of four distinct junctions in the father, who is acarrier of a balanced CCR. The proband inherited from the father both the abnormal chromosome 5 resulting in segmental aneusomies of chr5 (loss) and chr18 (gain) and a der(2) homologue. Evidences suggest a chromoplexy mechanism for this CCR derivation, involving double-strand breaks (DSBs) repaired by non-homologous end joining (NHEJ) or alternative end joining (alt-EJ). The complexity of the CCR and the segregation of homologues elucidate the genetic model for this family. This study demonstrates the importance of combining multiple genomic technologies to uncover genetic causes of complex neurodevelopmental syndromes and to better understand genetic disease mechanisms.

Analysis of Plasmids of the Klebsiella pneumoniae Complex Carrying a Cluster of Aerobactin Synthesis Genes as Presented in International Databases

Background. Currently, it is customary to distinguish two pathotypes of Klebsiella pneumoniae — classical and hypervirulent, which have the ability to cause community-acquired infections in healthy people. It has been shown that an increase in virulence is associated with the acquisition of additional genetic material — a plasmid carrying a cluster of aerobactin genes. Aim. To assess the prevalence of the aforementioned virulent plasmids around the globe and in Russia in particular, as well as to identify their key genetic features. Materials and methods. Plasmid sequences were downloaded from PLSDB and BV-BRC databases, annotated with the Abricate and Kleborate programs; cluster analysis was performed using the mge-cluster program, and phylogenetic analysis was performed using the Parsnp program. Results. 296 plasmid sequences isolated from 23 countries from clinical isolates of K.pneumoniae between 2006 and 2021 with a peak in 2019 were analyzed, with more than half of the plasmids coming from China. More than 30 sequence types were identified, among which ST11 and ST23 were predominant. Replicon genes of the IncFIB group were identified in almost all plasmids studied. The pre dominant type of aerobactin in the studied sequences was the first type (iuc1); sequences with iuc3 and iuc5 were also identified. Salmochelin synthesis genes were identified in only 37.1% of sequences; the yersiniabactin cluster was identified in two plasmids from China. 32.1% of plasmids carried resistance genes, of which 7.4% carried extended-spectrum beta-lactase genes and 5% contained carbapenemase genes. Nine clusters of sequences were obtained; almost all plasmids from Russia were assigned to one cluster and were NDM-positive. Together with plasmids from other European countries (Great Britain, Norway, Czech Republic), they formed a separate branch on the phylogenetic tree. Conclusion. Virulent plasmids carrying the aerobactin synthesis gene cluster are distributed globaly, and almost a third of them also carry antibiotic resistance genes.

Convergence of multiple resistance and hypervirulence in Klebsiella pneumoniae

Since 2018, Klebsiella pneumoniae isolates have been described in Russia, demonstrating the convergence of hypervirulent properties and multiple antibiotic resistance. The problem of the Klebsiella hypervirulent pathotype has been actualized relatively recently that was progressively described in the 1980s in the Pacific region. These Klebsiella spp. can cause serious community-acquired infections in healthy people, which fundamentally differs from the classic Klebsiella pathotype initially preserving sensitivity to most antibacterial drugs. In 20182020, there were reported detection of hypervirulent K. pneumoniae isolates in the Russian Federation. Like multiple resistance, hypervirulence is associated with the acquiring additional genetic material and formation of genetic lineages that effectively support such acquired determinants. For a long time, it was believed that the convergence of multiple resistance and hypervirulence is unlikely due to a large genetic burden as well as different ecological strategies in same species. The spread of hypervirulent strains, primarily in the Asian region, is associated with the conserved plasmids of the pLVPK group. The conservatism of both the originally discovered virulence plasmids (such as pLVPK and pK2044) and the genetic lineages associated with them (mainly CG23) is probably determined by the absence of a gene cluster responsible for conjugation in these plasmids. The driver of the spread of non-conjugative plasmids with determinants of hypervirulence is clonal spread, not horizontal gene transfer. Nevertheless, after a sufficiently long period of circulation of plasmids bearing markers of hypervirulence (described since 1986) in Klebsiella, a relatively limited number of genetic lineages, there were events of mobilization of the determinants of hypervirulence and, as a consequence, the inclusion in horizontal gene transfer in the population (described cases in 2016 ), which led to a sharp increase in the number of genetic lineages and variants of genetic platforms carrying hypervirulence genes. In Russia, first cases of hv-MDR-Kpn were described in 2018 in Moscow based on analyzing collection of Klebsiella isolated in 20122016. In 2020 and 2021, similar cases were described in St. Petersburg. In case of repeated pessimistic scenario observed over the last decade due to spread of carbapenemases, effectiveness of health care will be more than substantially harmed.

The Significance of Chromosome 11 Abnormalities in Patients with AML

Introduction: At the time of diagnosis AML the finding of KMT2A gene rearrangement qualifies patient to the group with adverse cytogenetic risk according to ELN 2017. In many hematooncological diseases including AML abnormalities concerning another regions of chromosome 11 are detected. However, their significance for outcome, CR rate, OS is still unknown. The main aim of this study was analysis of chromosome 11 abnormalities in AML patients, focusing on these without KMT2A gene rearrangement and its influence on patients outcome.Methods: Karyotype analysis from bone marrow aspirate was performed for patients with chromosome 11 abnormalities (abn11, n=36) and compared to two groups: with complex (CK, n=20) and normal karyotype (NK, n=44). The basic clinical and laboratory data including cytogenetic (karyotype and FISH method) and presence of TP53 deletion were analyzed to characterize in detail the group of patients with chromosome 11 abnormalities.Patients were treated with intensive chemotherapy, in 33% of them allogeneic cell transplantation (alloHCT) was performed.Results: In patients with abn11 the most frequent type of aberration was translocation, 11q23(+)/KMT2A(-) and 11q10-25 as a main region involved in aberrations, with minimal narrowing of region to 11q22. In patients with abn11 and translocation (excluding t(9;11)) there was higher frequency occurrence of 1 to 2 additional abnormalities (p=0.033) and lower frequency of complex karyotype existence (p=0.026). The gain of genetic material from chromosome 11 was observed in 33% of patients with abn11 group and the minimal amplified region was 11q22. Furthermore, in patients with amplification of chromosome 11 region, different additional cytogenetic abnormalities (such as monosomy 5 (p=0.045) and 18 (p<0.001)) were found in comparison to patients with other abnormalities of chromosome 11. Additional KMT2Agene copies were often observed in patients with 11q10-25 (p=0.013) and 11pter-qter (p=0.022) region involvement. The lowest frequency of TP53 deletion was in NK group (p=0.002) but comparable in patients with CK and abn11 without impact on OS and CR. The FISH analysis did not revealed KMT2A gene rearrangement in group with normal karyotype. There was particular attention to 11q23 region in patients with AML which enabled abnormality detection in GTG analysis, furthermore KMT2A rearrangement was confirmed or excluded by FISH method. In few cases FISH analysis allowed verification of KMT2A gene status in case of atypical hybrydization pattern occurrence.Leukocyte counts (p<0.001) and type of AML (de novo, secondary, therapy-related, p=0.022) differs in patients with abn11 in comparison to remained studied subgroups (Table 1.). The lowest blast percentage was observed in patients with 11p rearrangement (p=0.045). There were no significant differences in OS between all 3 groups of patients. CR was achieved in 15% in a CK group and it was significantly lower than in NK and abn11 group (p<0.001). Furthermore alloHCT improve OS in all treated patients (p<0.001). Additional genetic material from chromosome 11 occurrence had negative impact on OS (p<0.001) and CR (p=0.007). Patients with abn11 who achieved CR had lower median age (p=0.01) compared to these without CR. The lowest percentage of CR in abn11 group was observed in patients with additional KMT2A gene copies (p=0.008), 11q10-25 region involvement (p=0.036), HSR (homogeneously staining region) and aneuploidy (p=0.04).Conclusions: In summary, the most frequent region involved in chromosome 11 aberration was 11q22. Additional material derived from chromosome 11 had negative impact on CR and OS. Cytogenetic and molecular analysis in patients with AML are needed to detect most of abn11. In the era of targeted therapies their identification is very important to qualify the patient for more effective treatment. Both cytogenetic and molecular techniques widespread knowledge about cancer biology, however, classic cytogenetic is still “gold standard” and crucial method in AML diagnosis. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

High-Throughput Characterization of Cytogenomic Heterogeneity of MDS Using High-Resolution Optical Genome Mapping

IntroductionIntroduction of next-generation sequencing has defined the somatic mutational landscape in MDS. Comprehensive high-throughput structural variant profiling (SVP) is as important as mutation profiling in characterizing MDS clonal architecture since these large genomic aberrations have already shown to be critical for diagnosis and risk-stratification of MDS. A subset (MECOM, KMT2A rearrangements) are therapeutic targets in clinical trials. At this time, technical advances in SVP for copy number alterations (CNAs) and fusions have not been congruent with mutation profiling due to the inability of short-read (150bp) NGS to detect SVs. Currently available long-read (10-20Kbp) and whole genome sequencing cannot detect all SVs due to the presence of repeat sequences. Hence, conventional karyotyping (CK) remains the gold standard. Optical genome mapping (OGM) is a novel single-platform technique that measures ultra-long-range sequence patterns (>300Kbp), thereby unaffected by repeat sequences, enabling unbiased evaluation of all types of SVs at a high resolution. Here, we performed comprehensive SVP and mutation profiling in a large well-characterized cohort of MDS.MethodsWe selected samples with available fresh/frozen BM cells from consecutive treatment-naïve MDS pts who also underwent standard-of-care tests (CK, FISH, targeted 81-gene NGS for mutations). For OGM, ultra-high-molecular-weight-DNA was extracted, followed by labeling, linearization and imaging of DNA (Saphyr, Bionano) [median coverage:>300X]. The results were analyzed using de novo (>500 bp), rare variant (>5000 bp) and copy number (>500,000 bp) pipelines. The data was compared against 200 healthy controls to exclude common germline SVs. Clinical significance of the SVs was determined based on the location/overlap with the coding region of myeloid malignancy associated genes. The detection sensitivity was 10%.ResultsThere were 76 treatment naïve MDS patients. Baseline characteristics, comprehensive cytogenetic scoring system (CCSS) and R-IPPS risk categories and somatic mutations are in Fig 1.OGM identified all clonal abnormalities detected by CK [CNAs, inversions, inter/intra-chromosomal translocations, dicentric, complex derivative chromosomes]. Precise mapping of SVs by OGM at gene-level allowed determining the status of clinically informative biomarkers such as TET2, MECOM, TP53 and KMT2A, without the need for confirmatory assays. Detailed gene-level characterization of different SVs included KMT2A-ELL [t(11;19)] in MDS with WT1 mut, t(9;11) with SYTL2 fusion (and not KMT2A), der(1;7) leading to del(7q) in MDS with GATA2 mut/IDH2 mutand t(1;3)(p36;q21) rearrangements with potential PRDM16 disruption in SF3B1 mut/RUNX1 mutMDS, among others. Using OGM, we mapped the sequence patterns in both samples with IM with high level of confidence.Additionally, OGM identified 23 cryptic, clinically significant SVs in 14 (18%) of 76 pts. These included deletions of TET2, KMT2A, and del(5q), KMT2A amplification in MDS with FLT3-ITD/DNMT3A mut/RAS mut, NUP98-PRRX2, MECOM rearrangement in TET mut mutated NK-MDS. In addition, there were SVs of uncertain significance: duplications of chr1 (PDE41P), deletions of chr21 (involving RUNX1), chr2 (DNMT3A, ASXL2), chr12 (ETV6) and chr22 (EP300) and der(16)t(12;16)(q21.1;q12.1). These cryptic SVs were noted across all R-IPSS risk categories (highest yield in very-low and low R-IPSS) and across all cytogenetic risk-groups (very-good to very-poor).In complex karyotype setting, OGM could resolve the markers and additional genetic material, and in most cases, showed a much higher the degree of complexity within the genome than was apparent by CK. Four pts showed SV patterns typical of chromothripsis/chromoplexy.The median number of mutations per pt was 1 (0-6). When compared to mutation subsets, cryptic SVs were only identified in pts with ≤3 mutations. Majority represented either MDS with TP53 mut (6, 29%) or SF3B1 mut/TET mut (deletions of TET2, KMT2A, NOTCH1 and EP300 genes).ConclusionsUnbiased, high-throughput whole genome SVP revealed cryptic, clinically significant SVs in ~18% of MDS pts. OGM is a single-platform cytogenomic tool that can facilitate SVP at a gene-level resolution. This study provides strong support for further validation in expanded cohorts to guide clinical implementation and integration of SVP for routine work-up. [Display omitted] DisclosuresWei: Daiichi Sanko: Research Funding. Kantarjian: Ipsen Pharmaceuticals: Honoraria; Amgen: Honoraria, Research Funding; Astellas Health: Honoraria; Astra Zeneca: Honoraria; AbbVie: Honoraria, Research Funding; KAHR Medical Ltd: Honoraria; NOVA Research: Honoraria; Ascentage: Research Funding; Aptitude Health: Honoraria; Novartis: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Jazz: Research Funding; Immunogen: Research Funding; Daiichi-Sankyo: Research Funding; BMS: Research Funding; Precision Biosciences: Honoraria; Taiho Pharmaceutical Canada: Honoraria.

A Case of Partial Trisomy of 10q and Partial Monosomy of 6p Resulting from Maternal t(6;10) (p23;q24)

Chromosomal analysis is practiced routinely since long time in congenital malformations to find out structural and or numerical chromosomal aberrations. Translocation is one of the structural chromosomal aberrations where exchange of genetic material between the chromosomes is seen because of two breakpoints. On the basis of involvement of type of chromosome, two different types of translocation are defined. A case of two-year-old girl child with the history of developmental delay, generalised hypotonia and recurrent infections was reported whose cytogenetic analysis showed additional genetic material on ‘p’ arm of one chromosome 6. To find out the additional genetic material, parental chromosomal study was done which revealed balanced translocation between ‘q’ arm of chromosome 10 and ‘p’ arm of chromosome 6 and normal chromosomal pattern in father. Balanced translocation in mother gave rise to formation of derivative chromosome 6 which was transmitted to daughter causing partial trisomy of 10q and partial monosomy of 6p. This gain and loss of genetic material could be the cause of phenotypic features. In the current case, karyotyping was an investigation of choice and offering genetic counselling regarding prenatal diagnosis in future pregnancy was a thoughtful step.

Management tools for genetic diversity in an isolated population of the honeybee (

Context Beekeepers and honeybee queen breeders alike currently have few tools at their disposal for the management of genetic diversity inside their populations. Pedigree information is often absent, beekeepers cannot afford to genotype selection candidates due to costs, and acquisition of material for genotyping without risk to individual queen bees is difficult. However, in New World honeybee populations where import of additional genetic material to refresh the population is restricted (e.g. Australia) or impossible (e.g. New Zealand), management of genetic diversity is important for population sustainability. While the role of individual beekeepers in maintaining genetic resources becomes crucial under these circumstances, a more holistic approach to the management of genetic diversity is needed to allow for maximum impact of their contribution. Aims The establishment of affordable genotyping methodologies for successful strategies in managing honeybee genetic diversity, as well as the necessary delivery systems for the results to support the beekeeping community by providing interpretation in the context of the wider population. Methods Genotyping-by-sequencing of honeybee samples collected as part of a national survey were used as the basis for assessment of New Zealand’s honeybee genetic diversity and development of a tool with largely self-explanatory outputs that can be used directly by beekeepers. Key results It would appear that New Zealand’s honeybee population is sufficiently diverse to maintain population viability. However, both within regions and within companies, genetic diversity is significantly reduced, especially in the case of specialised queen breeders, indicating that active management will be necessary to achieve long-term sustainability. Conclusions Interactive tools are needed to help beekeepers understand their role in maintaining overall genetic diversity in the honeybee population as well as the potential impact of planned bee movement and queen acquisitions. Regular rounds of voluntary bee sampling can be used as the basis for management decisions without concentrating genotyping load on specific operators and restricting diversity assessments to subpopulations. Implications The described strategy is expected to both improve the outlook of New Zealand’s honeybee population as a whole and facilitate stringent genetic improvement programs by enabling queen breeders to make informed selection decisions and giving beekeepers confidence in the viability of their population.

How a microbe becomes a pandemic: a new story of the Black Death

In 2011, palaeogeneticists at McMaster University, Canada, and Tübingen University, Germany, reconstructed the genomes of Yersinia pestis, the causative organism of plague, from two 14th-century cemeteries below the centre of London.1,2 Since then, the Black Death and subsequent outbreaks of plague have been documented by additional genetic material—aDNA—retrieved from gravesites throughout Europe and southern Russia dating from the 14th to 18th centuries. One story this aDNA tells is that the most important event in plague history was not the Black Death, but something that preceded it: the Big Bang.

Prenatal identification of partial 3q duplication syndrome

BackgroundThe 3q duplication syndrome is a result of duplication of a large fragment of the long arm of chromosome 3, mainly 3q21-qter, and in most cases it is diagnosed only after birth. The phenotypic consequences resulting from genetic imbalance are an important source of information for genetic counselling, especially in prenatal diagnostics. However, in most cases it is impossible to define them precisely because the final clinical presentation is a result of an overlap, usually due to different sizes of deletions and/or duplications not only chromosome 3 but also of translocation partner chromosome. In this article, we present a prenatal diagnosis of the 3q duplication syndrome in a foetus, arising from a balanced insertion ins (7,3)(q21.2;q12.3q29) carried by the mother.Case presentationThe article presents a case of a 29-year-old woman referred to the Genetic Outpatient Clinic for consultation in the 12th week of her fifth pregnancy with a diagnosis of generalised hydrops foetalis. The analysis of karyotype using GTG technique and FISH allowed diagnosis of a balanced aberration in the mother, and determined the type of chromosomal rearrangement, which allowed the identification of the origin of the additional genetic material in the foetus and the previous malformed child of the same couple. The use of molecular karyotyping techniques (FISH and aCGH) allowed a precise determination of the size of the imbalanced fragments in the affected siblings.ConclusionsThe aCGH technique is particularly valuable for the diagnostics of submicroscopic deletions and duplications, if no imbalanced chromosomal aberrations are detected by routine cytogenetic tests. It is also a valuable technique for identifying and fully characterizing genetic material of unknown origin, which can’t be identified using routine cytogenetic techniqes. However, it does not allow identification of balanced aberrations in carriers.

B chromosome polymorphism in South American cichlid

Extra chromosomes are found in all major taxa, and their characteristics, function, and evolution are not yet completely understood. Known as B chromosomes, they are additional and dispensable genetic material that are present in particular individuals of certain populations of some species. In this work, we present the occurrence of B chromosomes in the cichlid Crenicichla lepidota from southern Brazil. The analyzed population showed 2n = 48 chromosomes, plus 0, 2, 3, or 4 B chromosomes, being variable among metaphases (intraindividual variation). Morphologically, these B chromosomes were variable in size, similarly to the A chromosomes. B chromosomes did not show heterochromatization. Other cytogenetic markers, such as Nucleolar Organizing Region, CMA3/DAPI base-specific dyes, and Fluorescent in situ hybridization with 18S rDNA probe, showed no differences in relation to previous studies with C. lepidota. Although this is the second description of B chromosomes for this species, we highlight the specific features of this population, especially the similarity to A chromosomes, in relation to size, morphology, and heterochromatin accumulation. In summary the B chromosomes described herein are large to small-sized, euchromatic chromosomes, a result that contrasts with that obtained so far for Neotropical cichlids.

Abstract 5693: Low coverage genome-wide sequencing of cell-free DNA enables detection, therapeutic monitoring, and characterization of copy number alterations in patients with solid tumors

Abstract Circulating tumor DNA (ctDNA) has been detected in the blood of patients with many cancer types and is thought to reflect the combined genetic profile of the primary tumor and metastases. The majority of studies into “liquid biopsies” have focused on detecting focal events including single nucleotide variants, fusions, and specific copy number alterations (CNAs); however, these assays are limited to mutations occurring in targeted regions and require deep sequencing. The objective of this study was to use low coverage, genome-wide sequencing of cell-free DNA (cfDNA) to evaluate the frequency, distribution, and persistence of genome-wide CNAs in the plasma of patients with solid tumors. cfDNA was isolated from a total of 203 plasma aliquots from 72 patients diagnosed with a variety of solid tumors. For almost half of the patients, multiple collections were available (range: 2-13) to enable longitudinal monitoring of treatment response. Greater than 25% of baseline cfDNA samples showed evidence of one or more CNAs and greater than 40% of patients had a CNA detected in at least one sample. Among patients with longitudinal monitoring, greater than 35% of individuals showed evidence of CNAs at baseline and approximately 25% of samples showed similar evidence in subsequent sampling. Collectively, CNAs were detected on all autosomes, suggesting that genome-wide profiling is necessary to fully assess CNA distributions. Additionally, we devised a metric which quantified the level of genomic instability. This metric, termed the genomic instability number (GIN), was associated with disease classification. In patients capable of longitudinal monitoring, GIN values were observed concomitant with therapeutic response (including, interestingly, response to immunotherapy) or disease progression and may provide information earlier than standard imaging-based methods. In addition, total cfDNA amount was evaluated as a predictor. When analysis was performed across all patients, there was a poor correlation between total cfDNA amount and the GIN; however, total cfDNA amount was strongly correlated with the cumulative abundance of CNA events within individual patients, suggesting that the CNAs detected in the cfDNA were derived from the additional genetic material contributed by the tumor. These data demonstrate the feasibility of detecting ctDNA in a significant portion of cancer patients solely on the basis of low coverage CNA profiling. Further, the nature of CNA events observed varied both between patients and across longitudinal samples from individual patients, suggesting potential for monitoring therapy response or disease progression. This study suggests that genome-wide CNA profiling may be useful alone or as a complement to standard variant detection strategies in the development of liquid biopsy technologies. Citation Format: Christopher K. Ellison, Aaron M. Goodman, Sabine Riethdorf, Amin R. Mazloom, Lisa Tran, Prachi Nakashe, Erin McCarthy, Tobias Gorges, Alexander Stein, Julia Quidde, Daniel S. Grosu, Mathias Ehrich, Taylor J. Jensen, Klaus Pantel, Razelle Kurzrock. Low coverage genome-wide sequencing of cell-free DNA enables detection, therapeutic monitoring, and characterization of copy number alterations in patients with solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5693. doi:10.1158/1538-7445.AM2017-5693

The Change of a Medically Important Genus: Worldwide Occurrence of Genetically Diverse Novel Brucella Species in Exotic Frogs.

The genus Brucella comprises various species of both veterinary and human medical importance. All species are genetically highly related to each other, sharing intra-species average nucleotide identities (ANI) of > 99%. Infections occur among various warm-blooded animal species, marine mammals, and humans. Until recently, amphibians had not been recognized as a host for Brucella. In this study, however, we show that novel Brucella species are distributed among exotic frogs worldwide. Comparative recA gene analysis of 36 frog isolates from various continents and different frog species revealed an unexpected high genetic diversity, not observed among classical Brucella species. In phylogenetic reconstructions the isolates consequently formed various clusters and grouped together with atypical more distantly related brucellae, like B. inopinata, strain BO2, and Australian isolates from rodents, some of which were isolated as human pathogens. Of one frog isolate (10RB9215) the genome sequence was determined. Comparative genome analysis of this isolate and the classical Brucella species revealed additional genetic material, absent from classical Brucella species but present in Ochrobactrum, the closest genetic neighbor of Brucella, and in other soil associated genera of the Alphaproteobacteria. The presence of gene clusters encoding for additional metabolic functions, flanked by tRNAs and mobile genetic elements, as well as by bacteriophages is suggestive for a different ecology compared to classical Brucella species. Furthermore it suggests that amphibian isolates may represent a link between free living soil saprophytes and the pathogenic Brucella with a preferred intracellular habitat. We therefore assume that brucellae from frogs have a reservoir in soil and, in contrast to classical brucellae, undergo extensive horizontal gene transfer.

Perspectivas de uso da hibridização genômica comparativa como rastreamento pré-implantacional em biópsias de embrião humano no estágio de blastocisto

Pre-implantation genetic screening could improve pregnancy rates in certain groups of patients with poor prognosis undergoing in vitro fertilization procedures. Recently its use as screening has been suggested aiming single embryo transfers. This paper evaluates comparative genomic hybridization technique, blastocyst stage embryo biopsy and analyzes the prospects of using both as pre-implantation genetic screening. A bibliographical review in scientific articles, books, journals and websites was done. Comparative genomic hybridization is able to analyze all chromosomes being promising as pre-implantation genetic screening. Blastocyst biopsy seems to be less aggressive to the embryo and provides additional genetic material compared to cleavage stage biopsies. The transfer of a genetically normal embryo increases pregnancy rates in in vitro fertilization procedures. However there are insufficient randomized controlled trials to ensure that comparative genomic hybridization in blastocysts cells has a practical impact in pregnancy rates.

A very rare cancer in Down syndrome: medulloblastoma. Epidemiological data from 13 countries

Persons with Down syndrome (DS) uniquely have an increased frequency of leukemias but a decreased total frequency of solid tumors. The distribution and frequency of specific types of brain tumors have never been studied in DS. We evaluated the frequency of primary neural cell embryonal tumors and gliomas in a large international data set. The observed number of children with DS having a medulloblastoma, central nervous system primitive neuroectodermal tumor (CNS-PNET) or glial tumor was compared to the expected number. Data were collected from cancer registries or brain tumor registries in 13 countries of Europe, America, Asia and Oceania. The number of DS children with each category of tumor was treated as a Poisson variable with mean equal to 0.000884 times the total number of registrations in that category. Among 8,043 neural cell embryonal tumors (6,882 medulloblastomas and 1,161 CNS-PNETs), only one patient with medulloblastoma had DS, while 7.11 children in total and 6.08 with medulloblastoma were expected to have DS. (p 0.016 and 0.0066 respectively). Among 13,797 children with glioma, 10 had DS, whereas 12.2 were expected. Children with DS appear to be specifically protected against primary neural cell embryonal tumors of the CNS, whereas gliomas occur at the same frequency as in the general population. A similar protection against neuroblastoma, the principal extracranial neural cell embryonal tumor, has been observed in children with DS. Additional genetic material on the supernumerary chromosome 21 may protect against embryonal neural cell tumor development.

Tackling Contentious Invasive Plant Species: A Case Study of Buffel Grass in Australia

Introduced plants that have both production values and negative impacts can be contentious. Generally they are either treated as weeds and their use prohibited; or unfettered exploitation is permitted and land managers must individually contend with any negative effects. Buffel grass (Cenchrus ciliaris) is contentious in Australia and there has been no attempt to broadly and systematically address the issues surrounding it. However, recent research indicates that there is some mutual acceptance by proponents and opponents of each others' perspectives and we contend that this provides the basis for a national approach. It would require thorough and on-going consultation with stakeholders and development of realistic goals that are applicable across a range of scales and responsive to regional differences in costs, benefits and socio-economic and biophysical circumstances. It would be necessary to clearly allocate responsibilities and ascertain the most appropriate balance between legislative and non-legislative mechanisms. A national approach could involve avoiding the introduction of additional genetic material, countering proliferation in regions where the species is sparse, preventing incursion into conservation reserves where it is absent, containing strategically located populations and managing communities to prevent or reduce dominance by buffel grass. This approach could be applied to other contentious plant species.

Chromosome Organizaton in Simple and Complex Unicellular Organisms

The genomes of unicellular organisms form complex 3-dimensional structures. This spatial organization is hypothesized to have a significant role in genomic function. Spatial organization is not limited solely to the three-dimensional folding of the chromosome(s) in genomes but also includes genome positioning, and the folding and compartmentalization of any additional genetic material (e.g. episomes) present within complex genomes. In this comment, I will highlight similarities in the spatial organization of eukaryotic and prokaryotic unicellular genomes.

Oxidant Pathway Functional Polymorphisms Influence the Risk of Myeloid Leukemia/Transient Myeloproliferative Disorder In Children with Down Syndrome.

AbstractAbstract 1680▪Individuals with Down syndrome have a 2% cumulative risk for the development of leukemia by the time they reach 30 years of age. In addition, as many as 5–10% of infants with Down syndrome may develop a transient myeloproliferative disorder (TMD). The molecular basis for the increased risk for hematologic disorders and other congenital developmental abnormalities with DS remains unknown. Additional genetic material from the critical Down syndrome locus at 21q22 includes the Cu/Zn superoxide dismutase gene and other genes contributing to high oxidative stress and increased endogenous DNA damage observed in cells from patients with Down syndrome. We hypothesized that functional polymorphic variants in enzymes associated with detoxification of oxidants and repair of oxidant associated DNA damage would be associated with an increased risk for the development of myeloid leukemia (ML) and TMD in children with Down syndrome. We studied the role of functional polymorphisms in the oxidant metabolizing genes, Paraoxonase 1 (PON1) and NADH/NADPH oxidase p22 phox (P22_PHOX) in the potential genetic etiology of ML/TMD in children with Down syndrome. Genotyping was conducted in 192 patients with Down Syndrome ML or TMD, and 251 healthy blood donor controls. All genotype frequencies in patients and control populations were consistent with those expected from Hardy-Weinberg equilibrium. We found that the variant PON1 Gln192Arg allele, associated with reduced free radical metabolism, occurred at a higher frequency in the Down syndrome ML/TMD population compared to healthy controls (OR, 2.71; 95% CI, 1.50–4.97; p=0.0003). Consistent with our hypothesis of increased oxidant sensitivity in these patients, we also observed decreased frequency of the protective variant P22_PHOX His72Tyr allele, purportedly associated with reduced generation of reactive oxygen species, in the Down syndrome ML/TMD population compared to healthy controls (OR, 0.48; 95% CI, 0.23–0.95; p=0.025). Notably, the variant PON1 Gln192Arg allele has also been associated with increased risk for non-Hodgkin's lymphoma in adults (Kerridge et al. Br J Haematol, 2002). Conclusion: These preliminary studies suggest that functional polymorphic variants in the oxidant metabolizing enzymes PON1 and P22_PHOX may influence risk for development of ML/TMD in children with Down syndrome. Studies to confirm these observations in a separate cohort of patients are in progress. Disclosures:No relevant conflicts of interest to declare.

Antibiotic resistance via the food chain: Fact or fiction?

The mechanisms that bacteria use to acquire additional genetic material, including genes coding for antibiotic resistance, are principally the secondary pathways that have been described as transformation and conjugation pathways. The farming industry often is reported as a hotspot for antibiotic-resistance reservoirs. In this review, we consider the exposure of food animals during the course of their lifespans to preventative, therapeutic or prophylactic treatment with antibiotic agents. In this context, zoonotic bacteria are commonly recognised as a potential threat to human health, with therapeutic treatment of pathogenic organisms on farms increasing the likelihood of selective antibiotic pressure influencing the commensal flora of the intestines. Existing literature indicates, however, that the effective impact on human health of such interventions in the food production process is still subject to debate.

Hybridization and introgression in Carex aquatilis and C. paleacea

The genetic relationships among the sedges Carex aquatilis, C. paleacea, and C. recta, and C. recta and other hybrids (C. aquatilis × recta and C. paleacea × recta) were investigated. Microsatellite-based, dominant inter simple sequence repeat (ISSR) fingerprinting revealed no taxon-specific variation among five investigated Carex species or hybrids, while in codominant microsatellite genotyping, 5 out of 16 alleles were taxon specific. Despite significant genetic differentiation, our results demonstrate that there is also gene flow between taxa. Although principal component analysis (PCA) showed some structuring among groups, there was considerable overlapping. The analysis of genetic differentiation assessed for the expected five groups using the program Structure did not provide conclusive results for the number of main groups. However, it is visible that C. aquatilis and C. paleacea are genetically distinct, while the other studied taxa show intermediate genetic features. Both the microsatellite analysis and sequencing of the internal transcribed spacer (ITS) region supported the view that the parental species of C. recta are C. aquatilis and C. paleacea, although with unequal contribution. C. paleacea × recta is likely to possess additional genetic material apart from that originating from C. aquatilis and C. paleacea. Our study shows that ISSR markers failed to be sufficiently informative, but the combination of sequencing (ITS) and the use of microsatellite genotyping proved their applicability in resolving fine-scale taxonomic questions.

Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity

BackgroundWhile the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study.ResultsThe two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms.ConclusionOverall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.