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The standard-of-care (SOC) diagnostic prenatal testing includes a combination of cytogenetic methods such as karyotyping, fluorescence in situ hybridization (FISH), and chromosomal microarray (CMA) using either direct or cultured amniocytes or chorionic villi sampling (CVS). However, each technology has its limitations: karyotyping has a low resolution (>5Mb), FISH is targeted, and CMA does not detect balanced structural variants (SVs) or decipher complex rearrangements in the genome. These limitations necessitate the use of multiple tests, either simultaneously or sequentially to reach a genetic diagnosis. This long-standing prenatal testing workflow demonstrates the need for an alternative technology that can provide high-resolution results in a cost and time-effective manner. Optical genome mapping (OGM) is an emerging technology that has demonstrated its ability to detect all classes of SVs, including copy number variations (CNVs) and balanced abnormalities in a single assay, but has not been evaluated in the prenatal setting. This retrospective validation study analyzed 114 samples (including replicates), representing 94 unique and well-characterized samples that were received in our laboratory for traditional cytogenetic analysis with karyotyping, FISH, and/or CMA. Samples comprised 84 cultured amniocytes, and 10 phenotypically normal and cytogenetically negative controls. Six samples were run in triplicate to evaluate intra-run, inter-run, and inter-instrument reproducibility. Clinically relevant SVs and CNVs were reported using the Bionano Access software with standardized and built-in filtration criteria and phenotype-specific analysis. OGM was 100% concordant in identifying the 101 aberrations that included 29 interstitial/terminal deletions, 28 duplications, 26 aneuploidies, 6 absence of heterozygosity (AOH), 3 triploid genomes, 4 Isochromosomes, 1 translocation, and revealed the identity of 3 marker chromosomes, and 1 chromosome with additional material not determined by karyotyping. Additionally, OGM detected 64 additional clinically reportable SVs in 43 samples. OGM demonstrated high technical and analytical robustness and a limit of detection of 5% allele fraction for interstitial deletions and duplications, and 10% allele fraction for translocation and aneuploidy. This study demonstrates that OGM has the potential to identify unique genomic abnormalities such as CNVs, AOHs, and several classes of SVs including complex structural rearrangements. OGM has a standardized laboratory workflow and reporting solution that can be adopted in routine clinical laboratories and demonstrates the potential to replace the current SOC methods for prenatal diagnostic testing. We recommend its use as a first-tier genetic diagnostic test in a prenatal setting.

Spatial neophobia and exploration are often assessed in nonhuman animals by measuring behavioral responses to novel environments. These traits may especially affect the performance of individuals translocated to novel environments for conservation purposes. Here, we present methods to administer and analyze a minimally invasive novel environment test that accounts for the social context of focal individuals. We used an aerial platform to capture video footage of a captive herd of scimitar-horned oryx (Oryx dammah) entering an unfamiliar enclosure. We analyzed footage for seven individually identifiable oryx, scoring their behavioral responses (i.e., latency to enter the enclosure, and movement and posture after entering the enclosure) and social context (i.e., relative position and number of nearby animals). We performed a principal components analysis (PCA) to explore individual traits and responses, and used generalized linear mixed models (GLMMs) to determine the effect of individual traits and social context on individual posture and movement behaviors. Both PCA and GLMMs supported our expectation that social context affects individual behavior: high neighbor density and relative position were negatively related to individual movement, and variation in social context was positively related with head-up postures and movement. Oryx were well differentiated along two principal components that reflected (1) vigilance or caution, and (2) changing social context and age. These methods provide a framework for assessing individual responses to a novel environment in a group setting, which can inform reintroduction and wildlife management efforts, while minimizing interference with animal behavior and management operations.

BACKGROUND: Type 1 diabetes (T1D) is associated with a greater risk of cardiovascular disease (CVD), mediated in part, by impaired nitric oxide (NO) bioavailability and endothelial dysfunction. In fact, women with T1D have a greater risk of CVD compared to men, and although the incidence of T1D is greater in Caucasians (Cs), African Americans (AAs) with T1D have significantly worse health outcomes. In healthy women, both resveratrol (RES) and antioxidants have been used to improve NO bioavailability and endothelial function by reducing oxidative stress. Accordingly, the present investigation sought to determine the role of resveratrol and antioxidants on vascular function in C and AA women with T1D. METHODS: 15 C women with T1D and 6 AA women with T1D were enrolled. Participants were randomized to either an acute dose of RES or an antioxidant cocktail (AOC) containing Vitamin C, Vitamin E, and Alpha-Lipoic Acid. The flow-mediated dilation (FMD) test, a bioassay of NO bioavailability, was utilized to assess endothelial function normalized for shear (FMD/Shear) before and after treatment. In addition, a venous blood sample was collected to assess baseline clinical laboratory values and plasma concentrations of oxidative stress (8-isoprostane (8-iso) and superoxide dismutase (SOD)) before and after treatment. Data are reported as mean ± SD. RESULTS: No differences in baseline demographics were observed between Cs and AAs. Clinical laboratory values were similar between groups, except HbA1c was higher ( p=0.013) in AAs (9.6±1.2%) compared to Cs (7.7±1.5%). Using a mixed model repeated measures design, a significant race x treatment x time interaction ( p=0.050) was observed for FMD/Shear. Treatment with AOC in AAs resulted in a significant increase ( p=0.002) in FMD/Shear. In addition, FMD/Shear was higher ( p=0.019) in AAs following treatment with AOC (0.370±0.128) compared to RES (0.212±0.049). Further, the % increase in FMD/Shear following treatment with AOC was greater ( p 1R01HL137087 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for faithful assignment of amino acids to their cognate tRNA. Variants in ARS genes are frequently associated with clinically heterogeneous phenotypes in humans and follow both autosomal dominant or recessive inheritance patterns in many instances. Variants in tryptophanyl-tRNA synthetase 1 (WARS1) cause autosomal dominantly inherited distal hereditary motor neuropathy and Charcot-Marie-Tooth disease. Presently, only one family with biallelic WARS1 variants has been described. We present three affected individuals from two families with biallelic variants (p.Met1? and p.(Asp419Asn)) in WARS1, showing varying severities of developmental delay and intellectual disability. Hearing impairment and microcephaly, as well as abnormalities of the brain, skeletal system, movement/gait, and behavior were variable features. Phenotyping of knocked down wars-1 in a C. elegans model showed depletion is associated with defects in germ cell development. A wars1 knockout vertebrate model recapitulates the human clinical phenotypes, confirms variant pathogenicity and uncovers evidence implicating the p.Met1? variant as potentially impacting an exon critical for normal hearing. Together, our findings provide consolidating evidence for biallelic disruption of WARS1 as causal for an autosomal recessive neurodevelopmental syndrome and present a vertebrate model that recapitulates key phenotypes observed in patients. This article is protected by copyright. All rights reserved.

Conventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, as well as microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. The use of OGM precludes the requirement for culturing (and related microbial contamination). However, a high percentage of MCC impedes a definitive diagnosis, which can be addressed by an additional pre-analytical quality control step that includes histological assessment of H&E stained slides from formalin-fixed paraffin embedded (FFPE) tissue with macro-dissection for chorionic villi to enrich fetal tissue component for single nucleotide polymorphism microarray (SNPM) analysis. To improve the diagnostic yield, an integrated workflow was devised that included MCC characterization of POC tissue, followed by OGM for MCC-negative cases or SNPM with histological assessment for MCC-positive cases. A result was obtained in 93% (29/31) of cases with a diagnostic yield of 45.1% (14/31) with the proposed workflow, compared to 9.6% (3/31) and 6.4% (2/31) with routine workflow, respectively. The integrated workflow with these technologies demonstrates the clinical utility and higher diagnostic yield in evaluating POC specimens.

Conventional cytogenetic analysis of products of conception (POC) is of limited utility because of failed cultures, microbial and maternal cell contamination (MCC). Optical genome mapping (OGM) is an emerging technology that has the potential to replace conventional cytogenetic methods. The use of OGM precludes the requirement for culturing (and related microbial contamination). However, a high percentage of MCC impedes a definitive diagnosis, which can be addressed by an additional pre-analytical quality control step that includes histological assessment of H&E stained slides from FFPE tissue with macro-dissection for Chorionic villi to enrich fetal tissue component for Single nucleotide polymorphism (SNP) microarray analysis. An internal audit of POC cases subjected to karyotype-only analysis showed a low yield on clinically actionable information that contributed to patient care. To improve the diagnostic yield, an integrated workflow was devised that included MCC characterization of POC tissue, followed by OGM for MCC negative cases or SNPM with histological assessment for MCC positive cases. A result was obtained in 93% (29/31) cases with a diagnostic yield of 45.1% (14/31) with proposed workflow compared to 9.6% (3/31) and 6.4% (2/31) with routine workflow, respectively. The integrated workflow with these technologies demonstrates the clinical utility and higher diagnostic yield in evaluating POC specimens.

Reconstruction of past changes in Arctic sea ice extent may be critical for understanding its future evolution. Methanesulfonate (MSA) and bromine concentrations preserved in ice cores have both been proposed as indicators of past sea ice conditions. In this study, two ice cores from central and north-eastern Greenland were analysed at sub-annual resolution for MSA (CH3SO3H) and bromine, covering the time period 1750–2010. We examine correlations between ice core MSA and the HadISST1 ICE sea ice dataset and consult back trajectories to infer the likely source regions. A strong correlation between the low-frequency MSA and bromine records during pre-industrial times indicates that both chemical species are likely linked to processes occurring on or near sea ice in the same source regions. The positive correlation between ice core MSA and bromine persists until the mid-20th century, when the acidity of Greenland ice begins to increase markedly due to increased fossil fuel emissions. After that time, MSA levels decrease as a result of declining sea ice extent but bromine levels increase. We consider several possible explanations and ultimately suggest that increased acidity, specifically nitric acid, of snow on sea ice stimulates the release of reactive Br from sea ice, resulting in increased transport and deposition on the Greenland ice sheet.

The sources and transport pathways of aerosol species in Antarctica remain uncertain, partly due to limited seasonally resolved data from the harsh environment. Here, we examine the seasonal cycles of major ions in three high-accumulation West Antarctic ice cores for new information regarding the origin of aerosol species. A new method for continuous acidity measurement in ice cores is exploited to provide a comprehensive, charge-balance approach to assessing the major non-sea-salt (nss) species. The average nss-anion composition is 41% sulfate (SO42−), 36% nitrate (NO3−), 15% excess-chloride (ExCl−), and 8% methanesulfonic acid (MSA). Approximately 2% of the acid-anion content is neutralized by ammonium (NH4+), and the remainder is balanced by the acidity (Acy ≈ H+ − HCO3−). The annual cycle of NO3− shows a primary peak in summer and a secondary peak in late winter/spring that are consistent with previous air and snow studies in Antarctica. The origin of these peaks remains uncertain, however, and is an area of active research. A high correlation between NH4+ and black carbon (BC) suggests that a major source of NH4+ is midlatitude biomass burning rather than marine biomass decay, as previously assumed. The annual peak in excess chloride (ExCl−) coincides with the late-winter maximum in sea ice extent. Wintertime ExCl− is correlated with offshore sea ice concentrations and inversely correlated with temperature from nearby Byrd station. These observations suggest that the winter peak in ExCl− is an expression of fractionated sea-salt aerosol and that sea ice is therefore a major source of sea-salt aerosol in the region.

Assessments of climate sensitivity to projected greenhouse gas concentrations underpin environmental policy decisions, with such assessments often based on model simulations of climate during recent centuries and millennia1, 2, 3. These simulations depend critically on accurate records of past aerosol forcing from global-scale volcanic eruptions, reconstructed from measurements of sulphate deposition in ice cores4, 5, 6. Non-uniform transport and deposition of volcanic fallout mean that multiple records from a wide array of ice cores must be combined to create accurate reconstructions. Here we re-evaluated the record of volcanic sulphate deposition using a much more extensive array of Antarctic ice cores. In our new reconstruction, many additional records have been added and dating of previously published records corrected through precise synchronization to the annually dated West Antarctic Ice Sheet Divide ice core7, improving and extending the record throughout the Common Era. Whereas agreement with existing reconstructions is excellent after 1500, we found a substantially different history of volcanic aerosol deposition before 1500; for example, global aerosol forcing values from some of the largest eruptions (for example, 1257 and 1458) previously were overestimated by 20–30% and others underestimated by 20–50%.

We present a detailed comparison between subsequent versions of commercially available wavelength-scanned cavity ring-down water isotope analysers (L2120-i and L2130-i, Picarro Inc.). The analysers are used in parallel in a continuous mode by adaption of a low-volume flash evaporation module. Application of the analysers to ice-core analysis is assessed by comparison between continuous water isotope measurements of a glacial ice-core from Severnaya Zemlya with discrete isotope-ratio mass spectrometry measurements performed on parallel samples from the same ice-core. The great advances between instrument versions, particularly in the measurement of δ(2)H, allow the continuous technique to achieve the same high level of accuracy and precision obtained using traditional isotope spectrometry techniques in a fraction of the experiment time. However, when applied to continuous ice-core measurements, increased integration times result in a compromise of the achievable depth resolution of the ice-core records.

Volcanism is a natural climate forcing causing short-term variations in temperatures. Histories of volcanic eruptions are needed to quantify their role in climate variability and assess human impacts. We present two new seasonally resolved, annually dated non-sea-salt sulfur records from polar ice cores - WAIS Divide (WDC06A) from West Antarctica spanning 408 B.C.E. to 2003 C.E. and NEEM (NEEM-2011-S1) from Greenland spanning 78 to 1997 C.E. - both analyzed using high-resolution continuous flow analysis coupled to two mass spectrometers. The high dating accuracy allowed placing the large bi-hemispheric deposition event ascribed to the eruption of Kuwae in Vanuatu (previously thought to be 1452/1453 C.E. and used as a tie-point in ice core dating) into the year 1458/1459 C.E. This new age is consistent with an independent ice core timescale from Law Dome and explains an apparent delayed response in tree rings to this volcanic event. A second volcanic event is detected in 1453 C.E. in both ice cores. We show for the first time ice core signals in Greenland and Antarctica from the strong eruption of Taupo in New Zealand in 232 C.E. In total, 133 volcanic events were extracted from WDC06A and 138 from NEEM-2011-S1, with 50 ice core signals - predominantly from tropical source volcanoes - identified simultaneously in both records. We assess the effect of large bipolar events on temperature-sensitive tree ring proxies. These two new volcanic records, synchronized with available ice core records to account for spatial variability in sulfate deposition, provide a basis for improving existing time series of volcanic forcing.

International audience; We present the WD2014 chronology for the upper part (0–2850 m; 31.2 ka BP) of the West Antarctic Ice Sheet (WAIS) Divide (WD) ice core. The chronology is based on counting of annual layers observed in the chemical, dust and electrical conductivity records. These layers are caused by seasonal changes in the source, transport, and deposi-tion of aerosols. The measurements were interpreted manually and with the aid of two automated methods. We validated the chronology by comparing to two high-accuracy, absolutely dated chronologies. For the Holocene, the cos-mogenic isotope records of 10 Be from WAIS Divide and 14 C for IntCal13 demonstrated that WD2014 was consistently accurate to better than 0.5 % of the age. For the glacial period, comparisons to the Hulu Cave chronology demonstrated that WD2014 had an accuracy of better than 1 % of the age at three abrupt climate change events between 27 and 31 ka. WD2014 has consistently younger ages than Green-land ice core chronologies during most of the Holocene. For Published by Copernicus Publications on behalf of the European Geosciences Union. 770 M. Sigl et al.: The WAIS Divide deep ice core WD2014 chronology the Younger Dryas–Preboreal transition (11.595 ka; 24 years younger) and the Bølling–Allerød Warming (14.621 ka; 7 years younger), WD2014 ages are within the combined uncertainties of the timescales. Given its high accuracy, WD2014 can become a reference chronology for the Southern Hemisphere, with synchronization to other chronologies feasible using high-quality proxies of volcanism, solar activity , atmospheric mineral dust, and atmospheric methane concentrations.

Interior Antarctica is among the most remote places on Earth and was thought to be beyond the reach of human impacts when Amundsen and Scott raced to the South Pole in 1911. Here we show detailed measurements from an extensive array of 16 ice cores quantifying substantial toxic heavy metal lead pollution at South Pole and throughout Antarctica by 1889 - beating polar explorers by more than 22 years. Unlike the Arctic where lead pollution peaked in the 1970s, lead pollution in Antarctica was as high in the early 20 th century as at any time since industrialization. The similar timing and magnitude of changes in lead deposition across Antarctica, as well as the characteristic isotopic signature of Broken Hill lead found throughout the continent, suggest that this single emission source in southern Australia was responsible for the introduction of lead pollution into Antarctica at the end of the 19 th century and remains a significant source today. An estimated 660 €...t of industrial lead have been deposited over Antarctica during the past 130 years as a result of mid-latitude industrial emissions, with regional-to-global scale circulation likely modulating aerosol concentrations. Despite abatement efforts, significant lead pollution in Antarctica persists into the 21 st century.