Achievement of Target Gain Larger than Unity in an Inertial Fusion Experiment

On December 5, 2022, an indirect drive fusion implosion on the National Ignition Facility (NIF) achieved a target gain G_{target} of 1.5. This is the first laboratory demonstration of exceeding "scientific breakeven" (or G_{target}>1) where 2.05 MJ of 351 nm laser light produced 3.1 MJ of total fusion yield, a result which significantly exceeds the Lawson criterion for fusion ignition as reported in a previous NIF implosion [H. Abu-Shawareb et al. (Indirect Drive ICF Collaboration), Phys. Rev. Lett. 129, 075001 (2022)PRLTAO0031-900710.1103/PhysRevLett.129.075001]. This achievement is the culmination of more than five decades of research and gives proof that laboratory fusion, based on fundamental physics principles, is possible. This Letter reports on the target, laser, design, and experimental advancements that led to this result.

Lawson Criterion for Ignition Exceeded in an Inertial Fusion Experiment

For more than half a century, researchers around the world have been engaged in attempts to achieve fusion ignition as a proof of principle of various fusion concepts. Following the Lawson criterion, an ignited plasma is one where the fusion heating power is high enough to overcome all the physical processes that cool the fusion plasma, creating a positive thermodynamic feedback loop with rapidly increasing temperature. In inertially confined fusion, ignition is a state where the fusion plasma can begin "burn propagation" into surrounding cold fuel, enabling the possibility of high energy gain. While "scientific breakeven" (i.e., unity target gain) has not yet been achieved (here target gain is 0.72, 1.37 MJ of fusion for 1.92 MJ of laser energy), this Letter reports the first controlled fusion experiment, using laser indirect drive, on the National Ignition Facility to produce capsule gain (here 5.8) and reach ignition by nine different formulations of the Lawson criterion.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Functional Architecture of Deleterious Genetic Variants in the Genome of a Wrangel Island Mammoth

Woolly mammoths were among the most abundant cold-adapted species during the Pleistocene. Their once-large populations went extinct in two waves, an end-Pleistocene extinction of continental populations followed by the mid-Holocene extinction of relict populations on St. Paul Island ∼5,600 years ago and Wrangel Island ∼4,000 years ago. Wrangel Island mammoths experienced an episode of rapid demographic decline coincident with their isolation, leading to a small population, reduced genetic diversity, and the fixation of putatively deleterious alleles, but the functional consequences of these processes are unclear. Here, we show that a Wrangel Island mammoth genome had many putative deleterious mutations that are predicted to cause diverse behavioral and developmental defects. Resurrection and functional characterization of several genes from the Wrangel Island mammoth carrying putatively deleterious substitutions identified both loss and gain of function mutations in genes associated with developmental defects (HYLS1), oligozoospermia and reduced male fertility (NKD1), diabetes (NEUROG3), and the ability to detect floral scents (OR5A1). These data suggest that at least one Wrangel Island mammoth may have suffered adverse consequences from reduced population size and isolation.

Multiple Pulmonary Pleomorphic Adenomas of Unknown Primary

Introduction/Objective

The most common site of pleomorphic adenomas (PAs) is salivary glands, which behave as benign tumors and rarely metastasize. Primary PAs in lungs are exceedingly rare. We report a case of multiple PAs in lungs with an inconclusive origin.

Methods

A 65-year-old woman had a two-year history of numerous scattered bilateral well-circumscribed pulmonary nodules measuring up to 2.1 cm. She had no prior history of smoking, asbestos exposure and salivary gland diseases, and denied any symptoms. The latest chest computed tomography (CT) scan showed the two largest lower lobe nodules had mildly increased in size compared to two years before. The patient then underwent wedge resections.

Results

Grossly, the wedge resection specimens showed multiple well-circumscribed, pale tan, firm nodules. Microscopically, the nodules comprised cytologically bland nests of polygonal to plasmacytoid cells with eosinophilic cytoplasm, variably set in a myxoid matrix. Immunohistochemical stains demonstrated that the cells were positive for AE-1/AE-3, S-100, bcl-2 and SOX-10, and negative for chromogranin, smooth muscle actin, p63, calponin, PAX-8, CD34, CD31, HMB-45, melan-A, HHF-35, GATA-3, GFAP and RCC marker; TTF-1 highlighted entrapped pulmonary epithelium but the tumor cells were negative. These findings might suggest metastatic low grade PA from salivary glands. However, the patient’s follow-up examination by an otolaryngologist was normal; the CT scan of her chest and abdomen did not show any remarkable findings other than her lung nodules.

Conclusion

To our knowledge, this is the first reported case of multiple pulmonary PAs without a preceding primary.

It has raised questions about the pathogenesis of multiple PAs in lungs. Could PA present as multiple primary nodules in lungs? Could one primary pulmonary PA generate multiple satellite nodules in lungs? Do multiple primary pulmonary PAs have a different IHC profile than that of a single primary pulmonary PA? More research is needed.

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

Standardized identification of genotypes is necessary in animals that reproduce asexually and form large clonal populations such as coral. We developed a high-resolution hybridization-based genotype array coupled with an analysis workflow and database for the most speciose genus of coral, Acropora, and their symbionts. We designed the array to co-analyze host and symbionts based on bi-allelic single nucleotide polymorphisms (SNP) markers identified from genomic data of the two Caribbean Acropora species as well as their dominant dinoflagellate symbiont, Symbiodinium ‘fitti’. SNPs were selected to resolve multi-locus genotypes of host (called genets) and symbionts (called strains), distinguish host populations and determine ancestry of coral hybrids between Caribbean acroporids. Pacific acroporids can also be genotyped using a subset of the SNP loci and additional markers enable the detection of symbionts belonging to the genera Breviolum, Cladocopium, and Durusdinium. Analytic tools to produce multi-locus genotypes of hosts based on these SNP markers were combined in a workflow called the Standard Tools for Acroporid Genotyping (STAG). The STAG workflow and database are contained within a customized Galaxy environment (https://coralsnp.science.psu.edu/galaxy/), which allows for consistent identification of host genet and symbiont strains and serves as a template for the development of arrays for additional coral genera. STAG data can be used to track temporal and spatial changes of sampled genets necessary for restoration planning and can be applied to downstream genomic analyses. Using STAG, we uncover bi-directional hybridization between and population structure within Caribbean acroporids and detect a cryptic Acroporid species in the Pacific.

P4522Intravascular volume expansion mitigates the impact of impaired renal function and associated clinical outcomes in chronic heart failure

Background/Introduction

Intravascular volume is regulated by the kidneys but the interconnection of the extent of volume expansion with renal function and outcomes in patients with chronic HF has not been assessed. Therefore, we evaluated how GFR-defined renal function and HF-related clinical outcomes are impacted by the relative extent of intravascular volume expansion. Our hypothesis was that greater rather than lesser volume expansion would be protective of worse renal function and contribute to better clinical outcomes than mild-moderate volume expansion.

Purpose

Assess the impact of quantitated intravascular volume expansion on heart failure (HF) outcomes in relation to renal function in post-hospital clinically determined “euvolemic” chronic HF patients.

Methods

Blood volume (BV) was prospectively measured in 87 HF patients considered clinically “euvolemic” post-diuresis at the time of hospital discharge using a standardized radiolabeled albumin indicator-dilution technique (Daxor Corp., NY, NY). A volume cut-point of ≥+25% above normal expected BV was used to define the greater degree of volume expansion from more mild-moderate expansion. These volume subgroups were then stratified by cohort median eGFR (46 mL/min/1.73m2) and analyzed for 1-year outcomes of HF-related mortality or 1st re-hospitalization using the Kaplan-Meier method.

Results

Volume expansion ≥+25% was demonstrated in 53% of the cohort at the time of hospital discharge despite hospital diuretic therapy. In this subgroup over 1.0 year of follow-up the risk for the composite outcome was significantly lower than in the group with mild-moderate volume expansion (Log-Rank p=0.017). Further, in the clinical setting of greater volume expansion, worse renal function with eGFR below the cohort median (<46 mL/min/1.73m2) was not associated with increased risk for the composite end-point (Figure). In contrast, low eGFR in the presence of mild-moderate volume expansion stratified risk and was associated with worse outcome relative to a higher eGFR above the median (Figure).

Figure 1

Conclusions

In post-hospital chronic HF patients significant intravascular volume expansion is common, and importantly the extent of BV expansion impacts outcomes including HF-related mortality. However, greater rather than lesser volume expansion appears to favorably mitigate the impact of worse renal function (low eGFR), while normal or mild-moderate expansion does not spare the impact of worse renal function on outcomes. Thus, a favorable degree of volume expansion appears to balance the risks of worse renal function. Volume-kidney interconnections are complex with volume status modulating the impact of impaired renal function on outcomes in chronic HF.

Acknowledgement/Funding

None

Seasonal temperature patterns and durations of acceptable temperature range in houses in Brisbane, Australia

A paradigm shift to the use of indoor rather than outdoor temperature to estimate the exposure risk of low and high temperatures is vital for better prediction of temperature health effects and timely health warnings, and will also assist in understanding the influence of temperature on energy consumption and comfort. This study aimed to quantify the percentage of hours during the year that indoor temperature (living room) was in the extended comfort band (18-28 °C) of a subtropical climate, and identify the diurnal pattern of indoor temperatures in different seasons. Data used was collected in a previous study on the association between indoor and outdoor temperature. A k-shape cluster analysis resulted in two clusters of indoor temperature patterns for both weekdays and weekends. A bimodal pattern was identified during the cool season and a flat top pattern for the warm season, with many variations at weekends. These patterns can be attributed to the influence of cooling and heating processes depending on the season as well as occupancy, occupants' interference, and building materials. During the intermediate season, a sinusoidal pattern was observed for both weekdays and weekends because occupants likely relied on outdoor temperature conditions which were similar to those expected indoors without heating or cooling devices. The percentage of hours in which the indoor temperature of the houses ranged within the extended comfort band was 72-97% throughout the year, but for the coldest and hottest months it was 50-75%. These findings show that Brisbane residents are at possible risk of exposure to cold and hot temperatures due to the poor thermal performance of houses, and confirm that there is no standard indoor temperature pattern for all houses.

Protease-activated receptor-1 inhibits proliferation but enhances leukemia stem cell activity in acute myeloid leukemia

Eradication of leukemia stem cells (LSCs) is the ultimate goal of treating acute myeloid leukemia (AML). We recently showed that the combined loss of Runx1/Cbfb inhibited the development of MLL-AF9-induced AML. However, c-Kit⁺/Gr-1^- cells remained viable in Runx1/Cbfb-deleted cells, indicating that suppressing RUNX activity may not eradicate the most immature LSCs. In this study, we found upregulation of several hemostasis-related genes, including the thrombin-activatable receptor PAR-1 (protease-activated receptor-1), in Runx1/Cbfb-deleted MLL-AF9 cells. Similar to the effect of Runx1/Cbfb deletion, PAR-1 overexpression induced CDKN1A/p21 expression and attenuated proliferation in MLL-AF9 cells. To our surprise, PAR-1 deficiency also prevented leukemia development induced by a small number of MLL-AF9 leukemia stem cells (LSCs) in vivo. PAR-1 deficiency also reduced leukemogenicity of AML1-ETO-induced leukemia. Re-expression of PAR-1 in PAR-1-deficient cells combined with a limiting-dilution transplantation assay demonstrated the cell-dose-dependent role of PAR-1 in MLL-AF9 leukemia: PAR-1 inhibited rapid leukemic proliferation when there were a large number of LSCs, while a small number of LSCs required PAR-1 for their efficient growth. Mechanistically, PAR-1 increased the adherence properties of MLL-AF9 cells and promoted their engraftment to bone marrow. Taken together, these data revealed a multifaceted role for PAR-1 in leukemogenesis, and highlight this receptor as a potential target to eradicate primitive LSCs in AML.

A Comparative Study of the in vitro and in vivo Antiviral Activities of Acyclovir and Penciclovir

The antiviral properties of the compounds acyclovir (ACV) and penciclovir (PCV) have been compared in a number of in vitro and in vivo assays. In vitro, both compounds had good activity against herpes simplex virus type 1 (HSV-1) and varicella-zoster virus (VZV), although ACV showed statistically significant superiority. In addition, ACV had greater activity against herpes simplex virus type 2 (HSV-2), human cytomegalovirus (HCMV) and Epstein-Barr virus (EBV). We examined the effect of time of addition and removal of ACV and PCV under a variety of conditions and found similar results with the two compounds under most conditions. However, at a high multiplicity of infection, when all of the cells would be expected to be synchronously expressing large amounts of the viral thymidine kinase, short exposures to PCV appeared to be superior to similar exposures to ACV. In the HSV-1 zosteriform mouse model there was no significant difference between the activities of ACV and PCV, or its prodrug famciclovir (FCV), in once- or twice-daily treatment. The possible significance of these results and those previously reported on the activity of the compounds in humans is discussed.

Genome-wide analysis of signatures of selection in populations of African honey bees (Apis mellifera) using new web-based tools

Background

With the development of inexpensive, high-throughput sequencing technologies, it has become feasible to examine questions related to population genetics and molecular evolution of non-model species in their ecological contexts on a genome-wide scale. Here, we employed a newly developed suite of integrated, web-based programs to examine population dynamics and signatures of selection across the genome using several well-established tests, including F_ST, pN/pS, and McDonald-Kreitman. We applied these techniques to study populations of honey bees (Apis mellifera) in East Africa. In Kenya, there are several described A. mellifera subspecies, which are thought to be localized to distinct ecological regions.

Results

We performed whole genome sequencing of 11 worker honey bees from apiaries distributed throughout Kenya and identified 3.6 million putative single-nucleotide polymorphisms. The dense coverage allowed us to apply several computational procedures to study population structure and the evolutionary relationships among the populations, and to detect signs of adaptive evolution across the genome. While there is considerable gene flow among the sampled populations, there are clear distinctions between populations from the northern desert region and those from the temperate, savannah region. We identified several genes showing population genetic patterns consistent with positive selection within African bee populations, and between these populations and European A. mellifera or Asian Apis florea.

Conclusions

These results lay the groundwork for future studies of adaptive ecological evolution in honey bees, and demonstrate the use of new, freely available web-based tools and workflows (http://usegalaxy.org/r/kenyanbee) that can be applied to any model system with genomic information.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1712-0) contains supplementary material, which is available to authorized users.

Evaluation of the anterior chamber angle in keratoconus and normal subjects

PURPOSE

To evaluate the anterior chamber angle in keratoconus eyes by use of the Visante™ OCT and Orbscan™ II.

METHODS

Anterior chamber angle was measured with the Visante™ OCT and Orbscan™ II in 52 subjects, 26 KC subjects and 26 age and control subjects.

RESULTS

When comparing the nasal and temporal angles obtained with the two techniques no correlation was found (R(2) always below 0.01) in either the control subjects or in the KC subjects. Despite this, there was an overall statistically significant difference in mean anterior chamber angles (p<0.001) between Visante™ OCT and Orbscan™ II. There was no statistical difference (p>0.05) between nasal and temporal anterior chamber angles when comparing controls and KC subjects with either of the two instruments. In general, the Visante™ OCT gave a smaller estimate of the anterior chamber angle.

CONCLUSION

The values from the Visante™ OCT and Orbscan™ II cannot be interchanged since the difference in measurement of the anterior chamber angle was significantly different between the two instruments.

Identification of indels in next-generation sequencing data

BACKGROUND

The discovery and mapping of genomic variants is an essential step in most analysis done using sequencing reads. There are a number of mature software packages and associated pipelines that can identify single nucleotide polymorphisms (SNPs) with a high degree of concordance. However, the same cannot be said for tools that are used to identify the other types of variants. Indels represent the second most frequent class of variants in the human genome, after single nucleotide polymorphisms. The reliable detection of indels is still a challenging problem, especially for variants that are longer than a few bases.

RESULTS

We have developed a set of algorithms and heuristics collectively called indelMINER to identify indels from whole genome resequencing datasets using paired-end reads. indelMINER uses a split-read approach to identify the precise breakpoints for indels of size less than a user specified threshold, and supplements that with a paired-end approach to identify larger variants that are frequently missed with the split-read approach. We use simulated and real datasets to show that an implementation of the algorithm performs favorably when compared to several existing tools.

CONCLUSIONS

indelMINER can be used effectively to identify indels in whole-genome resequencing projects. The output is provided in the VCF format along with additional information about the variant, including information about its presence or absence in another sample. The source code and documentation for indelMINER can be freely downloaded from www.bx.psu.edu/miller_lab/indelMINER.tar.gz .

Polar bears exhibit genome-wide signatures of bioenergetic adaptation to life in the arctic environment

Polar bears (Ursus maritimus) face extremely cold temperatures and periods of fasting, which might result in more severe energetic challenges than those experienced by their sister species, the brown bear (U. arctos). We have examined the mitochondrial and nuclear genomes of polar and brown bears to investigate whether polar bears demonstrate lineage-specific signals of molecular adaptation in genes associated with cellular respiration/energy production. We observed increased evolutionary rates in the mitochondrial cytochrome c oxidase I gene in polar but not brown bears. An amino acid substitution occurred near the interaction site with a nuclear-encoded subunit of the cytochrome c oxidase complex and was predicted to lead to a functional change, although the significance of this remains unclear. The nuclear genomes of brown and polar bears demonstrate different adaptations related to cellular respiration. Analyses of the genomes of brown bears exhibited substitutions that may alter the function of proteins that regulate glucose uptake, which could be beneficial when feeding on carbohydrate-dominated diets during hyperphagia, followed by fasting during hibernation. In polar bears, genes demonstrating signatures of functional divergence and those potentially under positive selection were enriched in functions related to production of nitric oxide (NO), which can regulate energy production in several different ways. This suggests that polar bears may be able to fine-tune intracellular levels of NO as an adaptive response to control trade-offs between energy production in the form of adenosine triphosphate versus generation of heat (thermogenesis).

Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history

The Khoisan people from Southern Africa maintained ancient lifestyles as hunter-gatherers or pastoralists up to modern times, though little else is known about their early history. Here we infer early demographic histories of modern humans using whole-genome sequences of five Khoisan individuals and one Bantu speaker. Comparison with a 420 K SNP data set from worldwide individuals demonstrates that two of the Khoisan genomes from the Ju/’hoansi population contain exclusive Khoisan ancestry. Coalescent analysis shows that the Khoisan and their ancestors have been the largest populations since their split with the non-Khoisan population ~100–150 kyr ago. In contrast, the ancestors of the non-Khoisan groups, including Bantu-speakers and non-Africans, experienced population declines after the split and lost more than half of their genetic diversity. Paleoclimate records indicate that the precipitation in southern Africa increased ~80–100 kyr ago while west-central Africa became drier. We hypothesize that these climate differences might be related to the divergent-ancient histories among human populations.

The expansion of Bantu agriculturalists 3,800 years ago in sub-Saharan Africa established first contact with Khoisan hunter-gatherers living in parts of Southern Africa. Sequencing the genomes of five Namibian-Khoisan hunter-gatherers and one Bantu individual tells a tale of admixture and isolation in the early history of modern human populations.

Early CD3+/CD15+ peripheral blood leukocyte chimerism patterns correlate with long-term engraftment in non-malignant hematopoietic SCT

Following hematopoietic SCT (HSCT) for non-malignant disorders (NMDs) variable donor chimerism among lympho-hematopoietic lines may be observed. We retrospectively evaluated early post-HSCT, lineage-sorted (CD3+ and CD15+) peripheral blood leukocyte chimerism data to characterize patterns and assess for association with long-term CD15+ engraftment. 'Early' was defined as the first value obtained between days +14 and +42, 'late' as the last recorded value after day +90. 'High' donor chimerism was defined as 80% on either fraction at all time-points. Patients were classified into four subgroups with respect to early CD3+/CD15+ chimerism patterns (high/low) then analyzed for long-term CD15+ chimerism status. A total of 135 transplants were evaluable, with all three time-points available in 97. Underlying disease, graft source, patient age and conditioning intensity varied. 'Split' early chimerism (discordant high/low CD3+/CD15+ status) was common. Multivariable analysis revealed strong association between conditioning regimen and primary disease on early CD3+/CD15+ chimerism patterns and a dominant predictive effect of early CD15+ chimerism on long-term CD15+ donor engraftment (observed at median day +365). These data may guide real-time clinician decisions (restraint vs intervention, when available) when faced with unfavorable or unusual early lympho-hematopoietic chimerism patterns following HSCT for NMD.

Galaxy tools to study genome diversity

Background

Intra-species genetic variation can be used to investigate population structure, selection, and gene flow in non-model vertebrates; and due to the plummeting costs for genome sequencing, it is now possible for small labs to obtain full-genome variation data from their species of interest. However, those labs may not have easy access to, and familiarity with, computational tools to analyze those data.

Results

We have created a suite of tools for the Galaxy web server aimed at handling nucleotide and amino-acid polymorphisms discovered by full-genome sequencing of several individuals of the same species, or using a SNP genotyping microarray. In addition to providing user-friendly tools, a main goal is to make published analyses reproducible. While most of the examples discussed in this paper deal with nuclear-genome diversity in non-human vertebrates, we also illustrate the application of the tools to fungal genomes, human biomedical data, and mitochondrial sequences.

Conclusions

This project illustrates that a small group can design, implement, test, document, and distribute a Galaxy tool collection to meet the needs of a particular community of biologists.

Updates of the HbVar database of human hemoglobin variants and thalassemia mutations

HbVar (http://globin.bx.psu.edu/hbvar) is one of the oldest and most appreciated locus-specific databases launched in 2001 by a multi-center academic effort to provide timely information on the genomic alterations leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Database records include extensive phenotypic descriptions, biochemical and hematological effects, associated pathology and ethnic occurrence, accompanied by mutation frequencies and references. Here, we report updates to >600 HbVar entries, inclusion of population-specific data for 28 populations and 27 ethnic groups for α-, and β-thalassemias and additional querying options in the HbVar query page. HbVar content was also inter-connected with two other established genetic databases, namely FINDbase (http://www.findbase.org) and Leiden Open-Access Variation database (http://www.lovd.nl), which allows comparative data querying and analysis. HbVar data content has contributed to the realization of two collaborative projects to identify genomic variants that lie on different globin paralogs. Most importantly, HbVar data content has contributed to demonstrate the microattribution concept in practice. These updates significantly enriched the database content and querying potential, enhanced the database profile and data quality and broadened the inter-relation of HbVar with other databases, which should increase the already high impact of this resource to the globin and genetic database community.

Cardiac Ultrasound Findings in Infants with Severe (Hurler Phenotype) Untreated Mucopolysaccharidosis (MPS) Type I

BACKGROUND

Serious cardiac valve disease and left ventricular hypertrophy occur in most untreated older children with severe mucopolysaccharidosis type I. Although it is assumed that early intervention prevents these processes, evaluation of cardiac findings in these infants has not yet been reported.

METHODS

We reviewed echocardiograms of 13 untreated infants < 1 year of age with severe mucopolysaccharidosis type I who had undergone evaluation for hematopoietic cell transplantation. We recorded left ventricular chamber dimensions, septal and posterior wall thicknesses, ventricular function, and aortic sinus diameters. We evaluated mitral and aortic valves for increased thickness, regurgitation, and stenosis.

RESULTS

Average age (7M, 6F) was 221 (range 25-347) days. Left ventricular chamber dimension was ≥2 SD of normal in 3/13; wall thicknesses were ≥2 SD of normal in 2/13 infants. Systolic function was normal. Mitral valves were thickened in all infants; mitral regurgitation was present in 9/13, but significant in only three infants. Aortic valves were thickened in 10/13, but no infant had significant aortic regurgitation. Neither mitral nor aortic stenosis occurred. Aortic roots were dilated to ≥2 SD of normal in 5/13.

CONCLUSIONS

Characteristic cardiac features of severe mucopolysaccharidosis type I can be seen in infancy. Mitral and aortic valve thickening are nearly universally present, even in the youngest infants. In 20-30 % of infants, other abnormalities such as left ventricular dilation, increased wall thickness, and mild mitral/aortic regurgitation may occur. Aortic root dilation is a frequent finding. Early intervention with enzyme replacement therapy may minimize the incidence and severity of cardiac findings in these infants.

SUMMARY

Serious cardiac valve disease and left ventricular hypertrophy occur in most untreated older children with severe mucopolysaccharidosis type I. Although it is assumed that early intervention prevents these processes, evaluation of cardiac findings in these infants has not yet been reported. In our study of 13 infants with severe untreated MPS I < 1 year of age, mitral and aortic valve thickening was nearly universally present and aortic root dilation was frequent. Despite this, we found a lower incidence of left ventricular hypertrophy and both a lower incidence and milder expression of mitral and aortic valve dysfunction than previously reported in older children. These findings suggest that earlier intervention, including neonatal screening, may be of benefit to children with severe MPS I.

Loss of Fatty-Acid delta(6) desaturating ability in human mammary epithelial-cells that express an activated C-ha-ras oncogene

The synthesis of essential fatty acids (EFAs) that have been shown to inhibit breast cancer cell growth in vitro and tumor growth in animals requires desaturation at C-6 of linoleic or alpha-linolenic acid. This observation, combined with reports that many tumors and tumor cell lines are deficient in Delta(6) desaturation and/or contain low levels of 6-desaturated EFAs, has led to the suggestion that loss of Delta(6) desaturating ability is relevant to the process of malignant transformation. This study was undertaken in search of direct evidence that malignant transformation of mammary epithelial cells alters EFA metabolism. We used two cell lines derived from the spontaneously immortalized human mammary epithelial cell line MCF-10A and expressing either the c-Ha-ras protooncogene (MCF-10AneoN) or an activated c-Ha-ras oncogene (MCF-10AneoT), and a cell line immortalized by transfection of human mammary epithelial cells with SV40 T antigen. We compared these cell lines in terms of ability to convert EFAs (30 mu M) to other EFAs of the same family. MCF-10AneoT cells lose the ability to perform Delta(6) and Delta(4) desaturations, whereas MCF-10AneoN cells and the SV40 T antigen-transformed cell line do not. No significant changes in growth response to culture with 6-desaturated EFAs were noted for MCF-10AneoT cells compared with MCF-10AneoN and parental MCF-10A cells, suggesting that FA metabolism alone cannot account for the effects of EFAs on the growth of neoplastic and non-neoplastic mammary epithelial cells.

Some phenotype association tools in Galaxy: looking for disease SNPs in a full genome

This unit focuses on some of the tools available on the public Galaxy server that are useful for exploring possible associations between human genetic variants and phenotypes. We trace step-by-step through an example illustrating several methods for examining a single full-coverage genome to look for single-nucleotide polymorphisms (SNPs) that are either known to be associated with disease or suspected to have impact for other reasons. It makes use of public genomic data, tools designed specifically for working with variants, and also some general tools for text manipulation and operations on genomic coordinates.

Sequencing and analysis of a South Asian-Indian personal genome

BACKGROUND

With over 1.3 billion people, India is estimated to contain three times more genetic diversity than does Europe. Next-generation sequencing technologies have facilitated the understanding of diversity by enabling whole genome sequencing at greater speed and lower cost. While genomes from people of European and Asian descent have been sequenced, only recently has a single male genome from the Indian subcontinent been published at sufficient depth and coverage. In this study we have sequenced and analyzed the genome of a South Asian Indian female (SAIF) from the Indian state of Kerala.

RESULTS

We identified over 3.4 million SNPs in this genome including over 89,873 private variations. Comparison of the SAIF genome with several published personal genomes revealed that this individual shared ~50% of the SNPs with each of these genomes. Analysis of the SAIF mitochondrial genome showed that it was closely related to the U1 haplogroup which has been previously observed in Kerala. We assessed the SAIF genome for SNPs with health and disease consequences and found that the individual was at a higher risk for multiple sclerosis and a few other diseases. In analyzing SNPs that modulate drug response, we found a variation that predicts a favorable response to metformin, a drug used to treat diabetes. SNPs predictive of adverse reaction to warfarin indicated that the SAIF individual is not at risk for bleeding if treated with typical doses of warfarin. In addition, we report the presence of several additional SNPs of medical relevance.

CONCLUSIONS

This is the first study to report the complete whole genome sequence of a female from the state of Kerala in India. The availability of this complete genome and variants will further aid studies aimed at understanding genetic diversity, identifying clinically relevant changes and assessing disease burden in the Indian population.

Measurement of the proton-air cross section at √s=57 TeV with the Pierre Auger Observatory

We report a measurement of the proton-air cross section for particle production at the center-of-mass energy per nucleon of 57 TeV. This is derived from the distribution of the depths of shower maxima observed with the Pierre Auger Observatory: systematic uncertainties are studied in detail. Analyzing the tail of the distribution of the shower maxima, a proton-air cross section of [505±22(stat)(-36)(+28)(syst)] mb is found.

Revealing mammalian evolutionary relationships by comparative analysis of gene clusters

Many software tools for comparative analysis of genomic sequence data have been released in recent decades. Despite this, it remains challenging to determine evolutionary relationships in gene clusters due to their complex histories involving duplications, deletions, inversions, and conversions. One concept describing these relationships is orthology. Orthologs derive from a common ancestor by speciation, in contrast to paralogs, which derive from duplication. Discriminating orthologs from paralogs is a necessary step in most multispecies sequence analyses, but doing so accurately is impeded by the occurrence of gene conversion events. We propose a refined method of orthology assignment based on two paradigms for interpreting its definition: by genomic context or by sequence content. X-orthology (based on context) traces orthology resulting from speciation and duplication only, while N-orthology (based on content) includes the influence of conversion events. We developed a computational method for automatically mapping both types of orthology on a per-nucleotide basis in gene cluster regions studied by comparative sequencing, and we make this mapping accessible by visualizing the output. All of these steps are incorporated into our newly extended CHAP 2 package. We evaluate our method using both simulated data and real gene clusters (including the well-characterized α-globin and β-globin clusters). We also illustrate use of CHAP 2 by analyzing four more loci: CCL (chemokine ligand), IFN (interferon), CYP2abf (part of cytochrome P450 family 2), and KIR (killer cell immunoglobulin-like receptors). These new methods facilitate and extend our understanding of evolution at these and other loci by adding automated accurate evolutionary inference to the biologist's toolkit. The CHAP 2 package is freely available from http://www.bx.psu.edu/miller_lab.

A genome sequence resource for the aye-aye (Daubentonia madagascariensis), a nocturnal lemur from Madagascar

We present a high-coverage draft genome assembly of the aye-aye (Daubentonia madagascariensis), a highly unusual nocturnal primate from Madagascar. Our assembly totals ~3.0 billion bp (3.0 Gb), roughly the size of the human genome, comprised of ~2.6 million scaffolds (N50 scaffold size = 13,597 bp) based on short paired-end sequencing reads. We compared the aye-aye genome sequence data with four other published primate genomes (human, chimpanzee, orangutan, and rhesus macaque) as well as with the mouse and dog genomes as nonprimate outgroups. Unexpectedly, we observed strong evidence for a relatively slow substitution rate in the aye-aye lineage compared with these and other primates. In fact, the aye-aye branch length is estimated to be ~10% shorter than that of the human lineage, which is known for its low substitution rate. This finding may be explained, in part, by the protracted aye-aye life-history pattern, including late weaning and age of first reproduction relative to other lemurs. Additionally, the availability of this draft lemur genome sequence allowed us to polarize nucleotide and protein sequence changes to the ancestral primate lineage-a critical period in primate evolution, for which the relevant fossil record is sparse. Finally, we identified 293,800 high-confidence single nucleotide polymorphisms in the donor individual for our aye-aye genome sequence, a captive-born individual from two wild-born parents. The resulting heterozygosity estimate of 0.051% is the lowest of any primate studied to date, which is understandable considering the aye-aye's extensive home-range size and relatively low population densities. Yet this level of genetic diversity also suggests that conservation efforts benefiting this unusual species should be prioritized, especially in the face of the accelerating degradation and fragmentation of Madagascar's forests.