Publications

We maintain this section to inform interested users about independent scientific studies conducted on MetaSystems products. We assume no responsibility or liability regarding the accuracy or correct use of the information or statements provided by external authors. The conclusions or statements expressed in the publications listed are those of the external authors or researchers. The publications may involve user-specific adaptations of MetaSystems products. They are not intended for diagnostic use. For publications covered by the Intended Purpose of Metafer or Ikaros, please refer to the respective instructions for use (IFU).

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Cancer Genetics, 260, 23-29
January, 2022

Classification of fluorescent R-Band metaphase chromosomes using a convolutional neural network is precise and fast in generating karyograms of hematologic neoplastic cells

Beate Vajen, Siegfried Hänselmann, Friederike Lutterloh, Simon Käfer, Jennifer Espenkötter, Anna Beening, Jochen Bogin, Brigitte Schlegelberger, Gudrun Göhring

<p>Karyotype analysis has a great impact on the diagnosis, treatment and prognosis in hematologic neo-plasms. The identification and characterization of chromosomes is a challenging process and needs experienced personal. Artificial intelligence provides novel support tools. However, their safe and reliable application in diagnostics needs to be evaluated. Here, we present a novel laboratory approach to identify chromosomes in cancer cells using a convolutional neural network (CNN). The CNN identified the correct chromosome class for 98.8% of chromosomes, which led to a time saving of 42% for the karyotyping workflow. These results demonstrate that the CNN has potential application value in chromosome classification of hematologic neoplasms. This study contributes to the development of an automatic karyotyping platform.</p>

Digital object identifier (DOI): https://doi.org/10.1016/j.cancergen.2021.11.005

European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology, 40, 2171--2176
October, 2021

Performances of automated digital imaging of Gram-stained slides with on-screen reading against manual microscopy.

Fischer, Adrien, Azam, Nouria, Rasga, Lara, Barras, Valérie, Tangomo, Manuela, Renzi, Gesuele, Vuilleumier, Nicolas, Schrenzel, Jacques, Cherkaoui, Abdessalam

<p>The objective of this study was to evaluate the performances of the automated digital imaging of Gram-stained slides against manual microscopy. Four hundred forty-three identified Gram-stained slides were included in this study. When both methods agreed, we considered the results as correct, and no further examination was carried out. Whenever the methods gave discrepant results, we reviewed the digital images and the glass slides by manual microscopy to avoid incorrectly read smears. The final result was a consensus of multiple independent reader interpretations. Among the 443 slides analyzed in this study, 101 (22.8%) showed discrepant results between the compared methods. The rates of discrepant results according to the specimen types were 5.7% (9/157) for positive blood cultures, 42% (60/142) for respiratory tract specimens, and 22% (32/144) for sterile site specimens. After a subsequent review of the discrepant slides, the final rate of discrepancies dropped to 7.0% (31/443). The overall agreement between the compared methods and the culture results reached 78% (345/443) and 79% (349/443) for manual microscopy and automated digital imaging, respectively. According to culture results, the specificity for automated digital imaging and manual microscopy were 90.8% and 87.7% respectively. In contrast, sensitivity was 84.1% for the two compared methods. The discrepant results were mostly encountered with microorganism morphologies of rare occurrence. The results reported in this study emphasize that on-screen reading is challenging, since the recognition of morphologies on-screen can appear different as compared to routine manual microscopy. Monitoring of Gram stain errors, which is facilitated by automated digital imaging, remains crucial for the quality control of reported Gram stain results.</p>

Digital object identifier (DOI): 10.1007/s10096-021-04233-2

Radiation research
September, 2021

CytoRADx: A High-Throughput, Standardized Biodosimetry Diagnostic System Based on the Cytokinesis-Block Micronucleus Assay.

Capaccio, Chris, Perrier, Jay R., Cunha, Lídia, Mahnke, Ryan C., Lörch, Thomas, Porter, Michael, Smith, Chris L., Damer, Ken, Bourland, J. Daniel, Frizzell, Bart, Torelli, Jennifer, Vasquez, Marie, Brower, Jeremy B., Doyle-Eisele, Melanie, Taveras, Maria, Turner, Helen, Brenner, David J., Kowalski, Richard

<p>In a large-scale catastrophe, such as a nuclear detonation in a major city, it will be crucial to accurately diagnose large numbers of people to direct scarce medical resources to those in greatest need. Currently no FDA-cleared tests are available to diagnose radiation exposures, which can lead to complex, life-threatening injuries. To address this gap, we have achieved substantial advancements in radiation biodosimetry through refinement and adaptation of the cytokinesis-block micronucleus (CBMN) assay as a high throughput, quantitative diagnostic test. The classical CBMN approach, which quantifies micronuclei (MN) resulting from DNA damage, suffers from considerable time and expert labor requirements, in addition to a lack of universal methodology across laboratories. We have developed the CytoRADx™ System to address these drawbacks by implementing a standardized reagent kit, optimized assay protocol, fully automated microscopy and image analysis, and integrated dose prediction. These enhancements allow the CytoRADx System to obtain high-throughput, standardized results without specialized labor or laboratory-specific calibration curves. The CytoRADx System has been optimized for use with both humans and non-human primates (NHP) to quantify radiation dose-dependent formation of micronuclei in lymphocytes, observed using whole blood samples. Cell nuclei and resulting MN are fluorescently stained and preserved on durable microscope slides using materials provided in the kit. Up to 1,000 slides per day are subsequently scanned using the commercially based RADxScan™ Imager with customized software, which automatically quantifies the cellular features and calculates the radiation dose. Using less than 1 mL of blood, irradiated ex vivo, our system has demonstrated accurate and precise measurement of exposures from 0 to 8 Gy (90% of results within 1 Gy of delivered dose). These results were obtained from 636 human samples (24 distinct donors) and 445 NHP samples (30 distinct subjects). The system demonstrated comparable results during in vivo studies, including an investigation of 43 NHPs receiving single-dose total-body irradiation. System performance is repeatable across laboratories, operators, and instruments. Results are also statistically similar across diverse populations, considering various demographics, common medications, medical conditions, and acute injuries associated with radiological disasters. Dose calculations are stable over time as well, providing reproducible results for at least 28 days postirradiation, and for blood specimens collected and stored at room temperature for at least 72 h. The CytoRADx System provides significant advancements in the field of biodosimetry that will enable accurate diagnoses across diverse populations in large-scale emergency scenarios. In addition, our technological enhancements to the well-established CBMN assay provide a pathway for future diagnostic applications, such as toxicology and oncology.</p>

Digital object identifier (DOI): 10.1667/RADE-20-00030.1

The British journal of dermatology
January, 2021

COVID-19 related dermatosis in November 2019. Could this case be Italy's patient zero?

Gianotti, R., Barberis, M., Fellegara, G., Galván-Casas, C., Gianotti, E.

<p>Milan, the largest city in northern Italy, was one of the first European metropolitan areas to be affected by the COVID-19 pandemic. We analyzed skin biopsies of patients from Milan with dermatoses and positive PCR swabs for SARS-CoV-2 at different stages of the infection (1,2). The results were compared to skin biopsies of 20 COVID-19 non-diagnosed patients with dermatoses, who were at high-risk of COVID-19 infection.</p>

Digital object identifier (DOI): 10.1111/bjd.19804

Pediatric reports, 13, 9--14
December, 2020

Detection of New Translocation in Infant Twins with Concordant ALL and Discordant Outcome.

Bahoush, Golamreza, Vafapour, Maryam, Kariminejad, Roxana

<p>About 2-5% of acute lymphoblastic leukemia (ALL) cases in pediatric patients are infants with an unfavorable prognosis because of high relapse probability. Early detection of the disease is, therefore, very important. Despite the fact that leukemia in twins occurs rarely, more attention has been paid to it in genetic studies. In the present study, through cytogenetic testing, a special case of concordant ALL in monozygotic twins was presented with different outcomes. In spite of an acceptable initial consequence to medical treatment in twins, in another brother (Twin B), early relapse was observed. In the cytogenetic study, both twins expressed while twin A expressed No cases have previously reported this mutation. Whether this translocation has a protective role for leukemia with mixed-lineage leukemia (MLL) gene rearrangement is still unclear. The difference in the translocation identified in the identical twins is also subject to further investigations.</p>

Digital object identifier (DOI): 10.3390/pediatric13010002

Genes, 12
December, 2020

A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858).

Merlo, Manuel A., Portela-Bens, Silvia, Rodríguez, María E., García-Angulo, Aglaya, Cross, Ismael, Arias-Pérez, Alberto, García, Emilio, Rebordinos, Laureana

<p>aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species' chromosome dynamics and evolution.</p>

Digital object identifier (DOI): 10.3390/genes12010049

Journal of personalized medicine, 10
October, 2020

Radiation Biomarkers in Large Scale Human Health Effects Studies.

Moquet, Jayne, Rothkamm, Kai, Barnard, Stephen, Ainsbury, Elizabeth

Following recent developments, the RENEB network (Running the European Network of biological dosimetry and physical retrospective dosimetry) is in an excellent position to carry out large scale molecular epidemiological studies of ionizing radiation effects, with validated expertise in the dicentric, fluorescent hybridization (FISH)-translocation, micronucleus, premature chromosome condensation, gamma-H2AX foci and gene expression assays. Large scale human health effects studies present complex challenges such as the practical aspects of sample logistics, assay costs, effort, effect modifiers and quality control/assurance measures. At Public Health England, the dicentric, automated micronucleus and gamma-H2AX radiation-induced foci assays have been tested for use in a large health effects study. The results of the study and the experience gained in carrying out such a large scale investigation provide valuable information that could help minimise random and systematic errors in biomarker data sets for health surveillance analyses going forward.

Digital object identifier (DOI): 10.3390/jpm10040155

International journal of radiation biology, 96, 1263--1273
October, 2020

Comparison of inexperienced operators and experts in γH2A.X and 53BP1 foci assay for high-throughput biodosimetry approaches in a mass casualty incident.

Bucher, Martin, Duchrow, Lukas, Endesfelder, David, Roessler, Ute, Gomolka, Maria

<p>In case of population exposure by ionizing radiation, a fast and reliable dose assessment of exposed and non-exposed individuals is crucial important. In initial triage, physicians have to take fast decisions whom to treat with adequate medical care. In addition, worries about significant exposure can be taken away from hundreds to thousands non- or low exposed individuals. Studies have shown that the γH2A.X radiation-induced foci assay is a promising test for fast triage decisions. However, in a large-scale scenario most biodosimetry laboratories will quickly reach their capacity limit. The aim of this study was to evaluate the benefit of inexperienced experimenters to speed up the foci assay and manual foci scoring. The participants of two training courses performed the radiation-induced foci assay (γH2A.X) under the guidance of experts and scored foci (γH2A.X and 53BP1) on sham-irradiated and irradiated blood samples (0.05-1.5 Gy). The outcome of laboratory experiments and manual foci scoring by 26 operators with basic experience in laboratory work was statistically analyzed in comparison to the results from experts. Inexperienced operators prepared slides with significant dose-effects (0, 0.1 and 1.0 Gy) for semi-automatic microscopic analyses. Manual foci scoring by inexperienced scorer resulted in a dose-effect curve for γH2A.X, 53BP1 and co-localized foci. In addition, inexperienced scorers were able to distinguish low irradiation doses from unirradiated cells. While 53BP1 foci scoring was in accordance to the expert counting, differences between beginners and expert increased for γH2A.X or co-localized foci. In case of a large-scale radiation event, inexperienced staff is useful to support laboratories in slide preparation for semi-automatic foci counting as well as γH2A.X and 53BP1 manual foci scoring for triage-mode biodosimetry. Slides can be clearly classified in the non-, low- or high-exposed category.</p>

Digital object identifier (DOI): 10.1080/09553002.2020.1793024

Tuberculosis (Edinburgh, Scotland), 125, 101993
September, 2020

Machine-assisted interpretation of auramine stains substantially increases through-put and sensitivity of microscopic tuberculosis diagnosis.

Horvath, L., Hänselmann, S., Mannsperger, H., Degenhardt, S., Last, K., Zimmermann, S., Burckhardt, I.

Of all bacterial infectious diseases, infection by Mycobacterium tuberculosis poses one of the highest morbidity and mortality burdens on humans throughout the world. Due to its speed and cost-efficiency, manual microscopy of auramine-stained sputum smears remains a crucial first-line detection method. However, it puts considerable workload on laboratory staff and suffers from a limited sensitivity. Here we validate a scanning and analysis system that combines fully-automated microscopy with deep-learning based image analysis. After automated scanning, the system summarizes diagnosis-relevant image information and presents it to the microbiologist in order to assist diagnosis. We tested the benefit of the automated scanning and analysis system using 531 slides from routine workflow, of which 56 were from culture positive specimen. Assistance by the scanning and analysis system allowed for a higher sensitivity (40/56 positive slides detected) than manual microscopy (34/56 positive slides detected), while greatly reducing manual slide-analysis time from a recommended 5-15 min to around 10 s per slide on average.

Digital object identifier (DOI): 10.1016/j.tube.2020.101993

Applied and environmental microbiology, 86
August, 2020

3-Hydroxybutyrate Derived from Poly-3-Hydroxybutyrate Mobilization Alleviates Protein Aggregation in Heat-Stressed Herbaspirillum seropedicae SmR1.

Alves, Luis Paulo Silveira, Santana-Filho, Arquimedes Paixão, Sassaki, Guilherme Lanzi, de Oliveira Pedrosa, Fabio, Maltempi de Souza, Emanuel, Chubatsu, Leda Satie, Müller-Santos, Marcelo

Under conditions of carbon starvation or thermal, osmotic, or oxidative shock, mutants affected in the synthesis or mobilization of poly-3-hydroxybutyrate (PHB) are known to survive less well. It is still unclear if the synthesis and accumulation of PHB are sufficient to protect bacteria against stress conditions or if the stored PHB has to be mobilized. Here, we demonstrated that mobilization of PHB in SmR1 was heat-shock activated at 45°C. proton ( H) nuclear magnetic resonance spectroscopy (i.e., H-nuclear magnetic resonance) showed that heat shock increased amounts of 3-hydroxybutyrate (3HB) only in strains able to synthesize and mobilize PHB. SmR1 mutants unable to synthesize or mobilize PHB were more susceptible to heat shock and survived less well than the parental strain. When 100 mM 3-hydroxybutyrate was added to the medium, the Δ strain (an mutant unable to synthesize PHB) and the double mutant with deletion of both and (i.e., Δ ) (unable to mobilize PHB) showed partial rescue of heat adaptability (from 0% survival without 3HB to 40% of the initial viable population). Addition of 200 mM 3HB before the imposition of heat shock reduced protein aggregation to 15% in the Δ mutant and 12% in the Δ mutant. We conclude that SmR1 is naturally protected by 3HB released by PHB mobilization, while mutants unable to generate large amounts of 3HB under heat shock conditions are less able to cope with heat damage. Bacteria are subject to abrupt changes in environmental conditions affecting their growth, requiring rapid adaptation. Increasing the concentration of some metabolites can protect bacteria from hostile conditions that lead to protein denaturation and precipitation, as well as damage to plasma membranes. In this work, we demonstrated that under thermal shock, the bacterium depolymerized its intracellular stock polymer known as poly-3-hydroxybutyrate (PHB), rapidly increasing the concentration of 3-hydroxybutyrate (3HB) and decreasing protein precipitation by thermal denaturation. Mutant strains unable to produce or depolymerize PHB suffered irreparable damage during thermal shock, resulting in fast death when incubated at 45°C. Our results will contribute to the development of bacteria better adapted to high temperatures found either in natural conditions or in industrial processes. In the case of and other bacteria that interact beneficially with plants, the understanding of PHB metabolism can be decisive for the development of more-competitive strains and their application as biofertilizers in agriculture.

Digital object identifier (DOI): 10.1128/AEM.01265-20

Toxicology in vitro : an international journal published in association with BIBRA, 66, 104866
August, 2020

A comparative in vitro toxicity assessment of electronic vaping product e-liquids and aerosols with tobacco cigarette smoke.

Wieczorek, R., Phillips, G., Czekala, L., Trelles Sticken, E., O'Connell, G., Simms, L., Rudd, K., Stevenson, M., Walele, T.

The use of electronic vaping products (EVPs) continues to increase worldwide among adult smokers in parallel with accumulating information on their potential toxicity and relative safety compared to tobacco smoke. At this time, in vitro assessments of many widely available EVPs are limited. In this study, an in vitro battery of established assays was used to examine the cytotoxic (Neutral red uptake), genotoxic (In vitro micronucleus) and mutagenic (Bacterial reverse mutation) responses of two commercial EVPs (blu GO™ disposable and blu PLUS+™ rechargeable) when compared to smoke from a reference cigarette (3R4F). In total, 12 commercial products were tested as e-liquids and as aerosols. In addition, two experimental base liquids containing 1.2% and 2.4% nicotine were also assessed to determine the effect of flavour and nicotine on all three assays. In the bacterial reverse mutation (Ames) and in vitro micronucleus (IVM) assays, exposures to e-liquids and EVP aerosols, with and without nicotine and in a range of flavourings, showed no mutagenic or genotoxic effects compared to tobacco smoke. The neutral red uptake (NRU) assay showed significantly reduced cytotoxicity (P < .05) for whole undiluted EVP aerosols compared to tobacco smoke, which by contrast was markedly cytotoxic even when diluted. The reduced in vitro toxicological responses of the EVPs add to the increasing body of scientific weight-of-evidence supporting the role of high-quality EVPs as a harm reduction tool for adult smokers.

Digital object identifier (DOI): 10.1016/j.tiv.2020.104866

Molecular ecology
July, 2020

Adaptive divergence across Southern Ocean gradients in the pelagic diatom Fragilariopsis kerguelensis.

Postel, Ute, Glemser, Barbara, Salazar Alekseyeva, Katherine, Eggers, Sarah Lena, Groth, Marco, Glöckner, Gernot, John, Uwe, Mock, Thomas, Klemm, Kerstin, Valentin, Klaus, Beszteri, Bánk

The Southern Ocean is characterized by longitudinal water circulations crossed by strong latitudinal gradients. How this oceanographic background shapes planktonic populations is largely unknown, despite the significance of this region for global biogeochemical cycles. Here, we show, based on genomic, morphometric, ecophysiological and mating compatibility data, an example of ecotypic differentiation and speciation within an endemic pelagic inhabitant, the diatom Fragilariopsis kerguelensis. We discovered three genotypic variants, one present throughout the latitudinal transect sampled, the others restricted to the north and south, respectively. The latter two showed reciprocal monophyly across all three genomes and significant ecophysiological differences consistent with local adaptation, but produced viable offspring in laboratory crosses. The third group was also reproductively isolated from the latter two. We hypothesize that this pattern originated by an adaptive expansion accompanied by ecotypic divergence, followed by sympatric speciation.

Digital object identifier (DOI): 10.1111/mec.15554

Genes, 11
July, 2020

Deciphering the Impact of a Bacterial Infection on Meiotic Recombination in Arabidopsis with Fluorescence Tagged Lines.

Gratias, Ariane, Geffroy, Valérie

<p>Plants are under strong evolutionary pressure to maintain surveillance against pathogens. One major disease resistance mechanism is based on NB-LRR (NLR) proteins that specifically recognize pathogen effectors. The cluster organization of the NLR gene family could favor sequence exchange between NLR genes via recombination, favoring their evolutionary dynamics. Increasing data, based on progeny analysis, suggest the existence of a link between the perception of biotic stress and the production of genetic diversity in the offspring. This could be driven by an increased rate of meiotic recombination in infected plants, but this has never been strictly demonstrated. In order to test if pathogen infection can increase DNA recombination in pollen meiotic cells, we infected Fluorescent Tagged Lines (FTL) with the virulent bacteria . We measured the meiotic recombination rate in two regions of chromosome 5, containing or not an NLR gene cluster. In all tested intervals, no significant difference in genetic recombination frequency between infected and control plants was observed. Although it has been reported that pathogen exposure can sometimes increase the frequency of recombinant progeny in plants, our findings suggest that meiotic recombination rate in may be resilient to at least some pathogen attack. Alternative mechanisms are discussed.</p>

Digital object identifier (DOI): 10.3390/genes11070832

Health physics, 119, 52--58
July, 2020

Automated Dicentric Aberration Scoring for Triage Dose Assessment: 60Co Gamma Ray Dose-response at Different Dose Rates.

Subramanian, Uma, O'Brien, Brett, McNamara, Maureen, Romanyukha, Lyudmila, Bolduc, David L., Olsen, Cara, Blakely, William F.

<p>The objective of this study was to establish radiation dose-response calibration curves using automated dicentric scoring to support rapid and accurate cytogenetic triage dose-assessment. Blood was drawn from healthy human volunteers and exposed to Co gamma rays at several dose rates (i.e., 1.0, 0.6, and 0.1 Gy min). After radiation, the blood was placed for 2 h in a 37 °C incubator for repair. Blood was then cultured in complete media to which a mitogen (i.e., phytoghemagglutinin, concentration 4%) was added for 48 h. Colcemid was added to the culture at a final concentration of 0.2 μg mL after 24 h for the purpose of arresting first-division metaphase mitotics. Cells were harvested at the end of 48 h. Samples were processed using an automated metaphase harvester and automated microscope metaphase finder equipped with a suite of software including a specialized automated dicentric scoring application. The data obtained were used to create dose-response tables of dicentric yields. The null hypothesis that the data is Poisson-distributed could not be rejected at the significance level of α = 0.05 using results from a Shiny R Studio application (goodness-of-fit Poisson). Calibration curves based on linear-quadratic fits for Co gamma rays at the three different dose rates were generated using these data. The calibration curves were used to detect blind test cases. In conclusion, using the automated harvester and automated microscope metaphase finder with associated automated dicentric scoring software demonstrates high-throughput with suitable accuracy for triage radiation dose assessment.</p>

Digital object identifier (DOI): 10.1097/HP.0000000000001285

Science advances, 6, eabb3446
June, 2020

Molecular atlas of the adult mouse brain.

Ortiz, Cantin, Navarro, Jose Fernandez, Jurek, Aleksandra, Märtin, Antje, Lundeberg, Joakim, Meletis, Konstantinos

Brain maps are essential for integrating information and interpreting the structure-function relationship of circuits and behavior. We aimed to generate a systematic classification of the adult mouse brain based purely on the unbiased identification of spatially defining features by employing whole-brain spatial transcriptomics. We found that the molecular information was sufficient to deduce the complex and detailed neuroanatomical organization of the brain. The unsupervised (non-expert, data-driven) classification revealed new area- and layer-specific subregions, for example in isocortex and hippocampus, and new subdivisions of striatum. The molecular atlas further supports the characterization of the spatial identity of neurons from their single-cell RNA profile, and provides a resource for annotating the brain using a minimal gene set-a brain palette. In summary, we have established a molecular atlas to formally define the spatial organization of brain regions, including the molecular code for mapping and targeting of discrete neuroanatomical domains.

Digital object identifier (DOI): 10.1126/sciadv.abb3446

Genes, 11
June, 2020

Interstitial Telomeric Repeats Are Rare in Turtles.

Clemente, Lorenzo, Mazzoleni, Sofia, Pensabene Bellavia, Eleonora, Augstenová, Barbora, Auer, Markus, Praschag, Peter, Protiva, Tomáš, Velenský, Petr, Wagner, Philipp, Fritz, Uwe, Kratochvíl, Lukáš, Rovatsos, Michail

<p>Telomeres are nucleoprotein complexes protecting chromosome ends in most eukaryotic organisms. In addition to chromosome ends, telomeric-like motifs can be accumulated in centromeric, pericentromeric and intermediate (i.e., between centromeres and telomeres) positions as so-called interstitial telomeric repeats (ITRs). We mapped the distribution of (TTAGGG) repeats in the karyotypes of 30 species from nine families of turtles using fluorescence in situ hybridization. All examined species showed the expected terminal topology of telomeric motifs at the edges of chromosomes. We detected ITRs in only five species from three families. Combining our and literature data, we inferred seven independent origins of ITRs among turtles. ITRs occurred in turtles in centromeric positions, often in several chromosomal pairs, in a given species. Their distribution does not correspond directly to interchromosomal rearrangements. Our findings support that centromeres and non-recombining parts of sex chromosomes are very dynamic genomic regions, even in turtles, a group generally thought to be slowly evolving. However, in contrast to squamate reptiles (lizards and snakes), where ITRs were found in more than half of the examined species, and birds, the presence of ITRs is generally rare in turtles, which agrees with the expected low rates of chromosomal rearrangements and rather slow karyotype evolution in this group.</p>

Digital object identifier (DOI): 10.3390/genes11060657

mSystems, 5
June, 2020

Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics.

Zaborin, Alexander, Penalver Bernabe, Beatriz, Keskey, Robert, Sangwan, Naseer, Hyoju, Sanjiv, Gottel, Neil, Gilbert, Jack A., Zaborina, Olga, Alverdy, John C.

<p>The cecum is a unique region in the mammalian intestinal tract in which the microbiome is localized to two compartments, the lumen and the crypts. The microbiome within crypts is particularly important as it is in direct contact with lining epithelial cells including stem cells. Here, we analyzed the microbiome in cecum of mice using multiple techniques including metagenomics. The lumen microbiome comprised and whereas the crypts were dominated by and , and the mucus comprised a mixture of these 4 phyla. The lumen microbial functional potential comprised mainly carbon metabolism, while the crypt microbiome was enriched for genes encoding stress resistance. In order to determine how this structure, assembly, and function are altered under provocative conditions, we exposed mice to overnight starvation (S), antibiotics (A), and a major surgical injury (partial hepatectomy [H]), as occurs with major surgery in humans. We have previously demonstrated that the combined effect of this "SAH" treatment leads to a major disturbance of the cecal microbiota at the bottom of crypts in a manner that disrupts crypt cell homeostasis. Here, we applied the SAH conditions and observed a loss of compartmentalization in both composition and function of the cecal microbiome associated with major shifts in local physicochemical cues including decrease of hypoxia, increase of pH, and loss of butyrate production. Taken together, these studies demonstrated a defined order, structure, and function of the cecal microbiome that can be disrupted under provocative conditions such as major surgery and its attendant exposures. The proximal colon and cecum are two intestinal regions in which the microbiome localizes to two spatially distinct compartments, the lumen and crypts. The differences in composition and function of luminal and crypt microbiome in the cecum and the effect of physiological stress on their compartmentalization remain poorly characterized. Here, we characterized the composition and function of the lumen-, mucus-, and crypt-associated microbiome in the cecum of mice. We observed a highly ordered microbial architecture within the cecum whose assembly and function become markedly disrupted when provoked by physiological stress such as surgery and its attendant preoperative treatments (i.e., overnight fasting and antibiotics). Major shifts in local physicochemical cues including a decrease in hypoxia levels, an increase in pH, and a loss of butyrate production were associated with the loss of compositional and functional compartmentalization of the cecal microbiome.</p>

Digital object identifier (DOI): 10.1128/mSystems.00377-20

Scientific reports, 10, 6682
April, 2020

α-synuclein inclusions are abundant in non-neuronal cells in the anterior olfactory nucleus of the Parkinson's disease olfactory bulb.

Stevenson, Taylor J., Murray, Helen C., Turner, Clinton, Faull, Richard L. M., Dieriks, Birger V., Curtis, Maurice A.

Reduced olfactory function (hyposmia) is one of the most common non-motor symptoms experienced by those living with Parkinson's disease (PD), however, the underlying pathology of the dysfunction is unclear. Recent evidence indicates that α-synuclein (α-syn) pathology accumulates in the anterior olfactory nucleus of the olfactory bulb years before the motor symptoms are present. It is well established that neuronal cells in the olfactory bulb are affected by α-syn, but the involvement of other non-neuronal cell types is unknown. The occurrence of intracellular α-syn inclusions were quantified in four non-neuronal cell types - microglia, pericytes, astrocytes and oligodendrocytes as well as neurons in the anterior olfactory nucleus of post-mortem human PD olfactory bulbs (n = 11) and normal olfactory bulbs (n = 11). In the anterior olfactory nucleus, α-syn inclusions were confirmed to be intracellular in three of the four non-neuronal cell types, where 7.78% of microglia, 3.14% of pericytes and 1.97% of astrocytes were affected. Neurons containing α-syn inclusions comprised 8.60% of the total neuron population. Oligodendrocytes did not contain α-syn. The data provides evidence that non-neuronal cells in the PD olfactory bulb contain α-syn inclusions, suggesting that they may play an important role in the progression of PD.

Digital object identifier (DOI): 10.1038/s41598-020-63412-x

International journal of radiation biology, 96, 214--219
February, 2020

An alternative approach for the induction of premature chromosome condensation in human peripheral blood lymphocytes using mitotic Akodon cells.

Selvan Gnana Sekaran, Tamizh, Ricoul, Michelle, Brochard, Patricia, Herate, Cecile, Sabatier, Laure

The premature chromosome condensation (PCC) technique is used to study exposure to external radiation through the determination of chromosome fragments observed in interphase cells. The presence of large telomeric signals in CHO cells interferes with the detection of PCC fragments and the identification of dicentric chromosomes. We present an improved method for the fusion of G0-lymphocytes with mitotic cells (few chromosomes and weakly-staining telomeric sequences) to induce PCC in combination with rapid quantification of dicentric chromosomes and centric rings as an alternative to the classical CHO cell fusion technique. Whole blood from three healthy volunteers was γ-irradiated with 0, 2, or 4 Gy. Following a 24 h incubation post-exposure at 37 °C, chromosome spreads of isolated lymphocytes were prepared by standard PCC procedures using mitotic cells. The percentage of scorable fusions, measured by telomere/centromere (T/C) staining, for -induced PCC was higher than that for CHO-induced PCC, irrespective of radiation exposure. Importantly, both techniques gave the same result for biodosimetry evaluation. The mitotic cell-induced PCC fusion assay, in combination with the scoring of dicentric chromosomes and rings by T/C staining of G0-lymphocytes is a suitable alternative for fast and reliable dose estimation after accidental radiation exposure.

Digital object identifier (DOI): 10.1080/09553002.2019.1625493

Scientific reports, 10, 2899
February, 2020

A High Throughput Approach to Reconstruct Partial-Body and Neutron Radiation Exposures on an Individual Basis.

Shuryak, Igor, Turner, Helen C., Perrier, Jay R., Cunha, Lydia, Canadell, Monica Pujol, Durrani, Mohammad H., Harken, Andrew, Bertucci, Antonella, Taveras, Maria, Garty, Guy, Brenner, David J.

Biodosimetry-based individualized reconstruction of complex irradiation scenarios (partial-body shielding and/or neutron + photon mixtures) can improve treatment decisions after mass-casualty radiation-related incidents. We used a high-throughput micronucleus assay with automated scanning and imaging software on ex-vivo irradiated human lymphocytes to: a) reconstruct partial-body and/or neutron exposure, and b) estimate separately the photon and neutron doses in a mixed exposure. The mechanistic background is that, compared with total-body photon irradiations, neutrons produce more heavily-damaged lymphocytes with multiple micronuclei/binucleated cell, whereas partial-body exposures produce fewer such lymphocytes. To utilize these differences for biodosimetry, we developed metrics that describe micronuclei distributions in binucleated cells and serve as predictors in machine learning or parametric analyses of the following scenarios: (A) Homogeneous gamma-irradiation, mimicking total-body exposures, vs. mixtures of irradiated blood with unirradiated blood, mimicking partial-body exposures. (B) X rays vs. various neutron + photon mixtures. The results showed high accuracies of scenario and dose reconstructions. Specifically, receiver operating characteristic curve areas (AUC) for sample classification by exposure type reached 0.931 and 0.916 in scenarios A and B, respectively. R for actual vs. reconstructed doses in these scenarios reached 0.87 and 0.77, respectively. These encouraging findings demonstrate a proof-of-principle for the proposed approach of high-throughput reconstruction of clinically-relevant complex radiation exposure scenarios.

Digital object identifier (DOI): 10.1038/s41598-020-59695-9