The Dynamics of Abell 2125

We present 371 galaxy velocities in the field of the very rich cluster Abell 2125 (z~0.25). These were determined using optical spectroscopy collected over several years from both the WIYN 3.5m telescope and NOAO Mayall 4m telescope. Prior studies at a variety of wavelengths (radio, optical, and X-ray) have indicated that A2125 is a likely cluster-cluster merger, a scenario which we are able to test using our large velocity database. We identified 224 cluster galaxies, which were subjected to a broad range of statistical tests using both positional and velocity information to evaluate the cluster dynamics and substructure. The tests confirmed the presence of substructures within the Abell 2125 system at high significance, demonstrating that A2125 is a complex dynamical system. Comparison of the test results with existing simulations strengthens the merger hypothesis, and provides clues about the merger geometry and stage. The merger model for the system can reconcile A2125's low X-ray temperature and luminosity with its apparently high richness, and might also explain A2125's high fraction of active galaxies identified in prior radio and optical studies.Comment: 34 pages, including tables and 3 color figures; to appear in Ap

Inferring late-Holocene climate in the Ecuadorian Andes using a chironomid-based temperature inference model

Presented here is the first chironomid calibration data set for tropical South America. Surface sediments were collected from 59 lakes across Bolivia (15 lakes), Peru (32 lakes), and Ecuador (12 lakes) between 2004 and 2013 over an altitudinal gradient from 150 m above sea level (a.s.l) to 4655 m a.s.l, between 0–17◦ S and 64–78◦ W. The study sites cover a mean annual temperature (MAT) gradient of 25 ◦ C. In total, 55 chironomid taxa were identified in the 59 calibration data set lakes. When used as a single explanatory variable, MAT explains 12.9% of the variance (λ1/λ2 =1.431). Two inference models were developed using weighted averaging (WA) and Bayesian methods. The best performing model using conventional statistical methods was a WA (inverse) model (R2jack= 0.890; RMSEPjack= 2.404 ◦C, RMSEP – root mean jack squared error of prediction; mean biasjack = −0.017 ◦C; max biasjack = 4.665 ◦C). The Bayesian method produced a model with R2jack = 0.909, RMSEPjack = 2.373 ◦C, mean jack biasjack = 0.598 ◦C, and max biasjack = 3.158 ◦C. Both models were used to infer past temperatures from a ca. 3000-year record from the tropical Andes of Ecuador, Laguna Pindo. Inferred temperatures fluctuated around modern-day conditions but showed significant departures at certain intervals (ca. 1600 cal yr BP; ca. 3000–2500 cal yr BP). Both methods (WA and Bayesian) showed similar patterns of temperature variability; however, the magnitude of fluctuations differed. In general the WA method was more variable and often underestimated Holocene temperatures (by ca. −7 ± 2.5 ◦C relative to the modern period). The Bayesian method provided temperature anomaly estimates for cool periods that lay within the expected range of the Holocene (ca. −3 ± 3.4 ◦C). The error associated with both reconstructions is consistent with a constant temperature of 20 ◦C for the past 3000 years. We would caution, however, against an over-interpretation at this stage. The reconstruction can only currently be deemed qualitative and requires more research before quantitative estimates can be generated with confidence. Increasing the number, and spread, of lakes in the calibration data set would enable the detection of smaller climate signals

Ab Initio Modeling of the Herpesvirus VP26 Core Domain Assessed by CryoEM Density

Efforts in structural biology have targeted the systematic determination of all protein structures through experimental determination or modeling. In recent years, 3-D electron cryomicroscopy (cryoEM) has assumed an increasingly important role in determining the structures of these large macromolecular assemblies to intermediate resolutions (6–10 Å). While these structures provide a snapshot of the assembly and its components in well-defined functional states, the resolution limits the ability to build accurate structural models. In contrast, sequence-based modeling techniques are capable of producing relatively robust structural models for isolated proteins or domains. In this work, we developed and applied a hybrid modeling approach, utilizing cryoEM density and ab initio modeling to produce a structural model for the core domain of a herpesvirus structural protein, VP26. Specifically, this method, first tested on simulated data, utilizes the cryoEM density map as a geometrical constraint in identifying the most native-like models from a gallery of models generated by ab initio modeling. The resulting model for the core domain of VP26, based on the 8.5-Å resolution herpes simplex virus type 1 (HSV-1) capsid cryoEM structure and mutational data, exhibited a novel fold. Additionally, the core domain of VP26 appeared to have a complementary interface to the known upper-domain structure of VP5, its cognate binding partner. While this new model provides for a better understanding of the assembly and interactions of VP26 in HSV-1, the approach itself may have broader applications in modeling the components of large macromolecular assemblies

Environmental controls on the distribution and diversity of lentic Chironomidae (Insecta: Diptera) across an altitudinal gradient in tropical South America

To predict the response of aquatic ecosystems to future global climate change, data on the ecology and distribution of keystone groups in freshwater ecosystems are needed. In contrast to mid- and high-latitude zones, such data are scarce across tropical South America (Neotropics). We present the distribution and diversity of chironomid species using surface sediments of 59 lakes from the Andes to the Amazon (0.1–17°S and 64–78°W) within the Neotropics. We assess the spatial variation in community assemblages and identify the key variables influencing the distributional patterns. The relationships between environmental variables (pH, conductivity, depth, and sediment organic content), climatic data, and chironomid assemblages were assessed using multivariate statistics (detrended correspondence analysis and canonical correspondence analysis). Climatic parameters (temperature and precipitation) were most significant in describing the variance in chironomid assemblages. Temperature and precipitation are both predicted to change under future climate change scenarios in the tropical Andes. Our findings suggest taxa of Orthocladiinae, which show a preference to cold high-elevation oligotrophic lakes, will likely see range contraction under future anthropogenic-induced climate change. Taxa abundant in areas of high precipitation, such as Micropsectra and Phaenopsectra, will likely become restricted to the inner tropical Andes, as the outer tropical Andes become drier. The sensitivity of chironomids to climate parameters makes them important bio-indicators of regional climate change in the Neotropics. Furthermore, the distribution of chironomid taxa presented here is a vital first step toward providing urgently needed autecological data for interpreting fossil chironomid records of past ecological and climate change from the tropical Andes

Forests protect aquatic communities from detrimental impact by volcanic deposits in the tropical Andes (Ecuador)

Volcanic activity impacts ecosystems sometimes with multiple, complex and long-lasting consequences, including volcanic tephra (airborne material) causing widespread disruptions. We study the effects of tephra deposition around two tropical lakes of Ecuador using a multi-proxy analysis of lake sediment archives spanning the last 2000 years. We present the dynamics of terrestrial vegetation (pollen), aquatic macroinvertebrate fauna (chironomids) and organic matter (stable isotopes) in: (i) a high elevation, stream-connected, open alpine grassland (Andean páramo) and (ii) a mid-elevation, stream-isolated, pre-montane forest. Páramo vegetation showed a slight increase in herbs and quick recovery after the tephra deposition; however, the aquatic community suffered a regime shift not reversed today c. 1500 years after the event. In the pre-montane location, the canopy opened up following tephra deposition, and it took c. 150 years to return to pre-impact levels. At the forested site, no major changes in the aquatic fauna were observed related to the tephra deposition. We hypothesise that the forest acted as a protective barrier preventing a large fallout of ash into the aquatic system. Forest not only acted as a buffer for ash falling into the water from the air, but also prevented landslides of tephra by enhancing soil stability, contrary to what was observed in the open system. We demonstrate the protective ecosystem service that forests play in sustaining ecological resilience and water quality facing natural (volcanic) disturbance. The ongoing deforestation of tropical regions therefore might increase the vulnerability of aquatic ecosystems, threatening the water quality for ecosystems and human populations

Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits.

The cardiac transcription factor (TF) gene NKX2-5 has been associated with electrocardiographic (EKG) traits through genome-wide association studies (GWASs), but the extent to which differential binding of NKX2-5 at common regulatory variants contributes to these traits has not yet been studied. We analyzed transcriptomic and epigenomic data from induced pluripotent stem cell-derived cardiomyocytes from seven related individuals, and identified ~2,000 single-nucleotide variants associated with allele-specific effects (ASE-SNVs) on NKX2-5 binding. NKX2-5 ASE-SNVs were enriched for altered TF motifs, for heart-specific expression quantitative trait loci and for EKG GWAS signals. Using fine-mapping combined with epigenomic data from induced pluripotent stem cell-derived cardiomyocytes, we prioritized candidate causal variants for EKG traits, many of which were NKX2-5 ASE-SNVs. Experimentally characterizing two NKX2-5 ASE-SNVs (rs3807989 and rs590041) showed that they modulate the expression of target genes via differential protein binding in cardiac cells, indicating that they are functional variants underlying EKG GWAS signals. Our results show that differential NKX2-5 binding at numerous regulatory variants across the genome contributes to EKG phenotypes

Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics

Induced pluripotent stem cells (iPSCs) show variable methylation patterns between lines, some of which reflect aberrant differences relative to embryonic stem cells (ESCs). To examine whether this aberrant methylation results from genetic variation or non-genetic mechanisms, we generated human iPSCs from monozygotic twins to investigate how genetic background, clone, and passage number contribute. We found that aberrantly methylated CpGs are enriched in regulatory regions associated with MYC protein motifs and affect gene expression. We classified differentially methylated CpGs as being associated with genetic and/or non-genetic factors (clone and passage), and we found that aberrant methylation preferentially occurs at CpGs associated with clone-specific effects. We further found that clone-specific effects play a strong role in recurrent aberrant methylation at specific CpG sites across different studies. Our results argue that a non-genetic biological mechanism underlies aberrant methylation in iPSCs and that it is likely based on a probabilistic process involving MYC that takes place during or shortly after reprogramming

Aquatic community response to volcanic eruptions on the Ecuadorian Andean flank: evidence from the palaeoecological record

Aquatic ecosystems in the tropical Andes are under increasing pressure from human modification of the landscape (deforestation and dams) and climatic change (increase of extreme events and 1.5 °C on average temperatures are projected for AD 2100). However, the resilience of these ecosystems to perturbations is poorly understood. Here we use a multi-proxy palaeoecological approach to assess the response of aquatic ecosystems to a major mechanism for natural disturbance, volcanic ash deposition. Specifically, we present data from two Neotropical lakes located on the eastern Andean flank of Ecuador. Laguna Pindo (1°27.132′S–78°04.847′W) is a tectonically formed closed basin surrounded by a dense mid-elevation forest, whereas Laguna Baños (0°19.328′S–78°09.175′W) is a glacially formed lake with an inflow and outflow in high Andean Páramo grasslands. In each lake we examined the dynamics of chironomids and other aquatic and semi-aquatic organisms to explore the effect of thick (> 5 cm) volcanic deposits on the aquatic communities in these two systems with different catchment features. In both lakes past volcanic ash deposition was evident from four large tephras dated to c.850 cal year BP (Pindo), and 4600, 3600 and 1500 cal year BP (Baños). Examination of the chironomid and aquatic assemblages before and after the ash depositions revealed no shift in composition at Pindo, but a major change at Baños occurred after the last event around 1500 cal year BP. Chironomids at Baños changed from an assemblage dominated by Pseudochironomus and Polypedilum nubifer-type to Cricotopus/Paratrichocladius type-II, and such a dominance lasted for approximately 380 years. We suggest that, despite potential changes in the water chemistry, the major effect on the chironomid community resulted from the thickness of the tephra being deposited, which acted to shallow the water body beyond a depth threshold. Changes in the aquatic flora and fauna at the base of the trophic chain can promote cascade effects that may deteriorate the ecosystem, especially when already influenced by human activities, such as deforestation and dams, which is frequent in the high Andes

An Unusual Radio Galaxy in Abell 428: A Large, Powerful FR I Source in a Disk-Dominated Host

We report the discovery of a powerful (~10^{24} Watts/Hz) FR I radio source in a highly flattened disk-dominated galaxy. Half of the radio flux from this source is concentrated within the host galaxy, with the remainder in a pair of nearly symmetrical lobes with total extent ~200kpc nearly perpendicular to the disk. The traditional wisdom maintains that powerful, extended radio sources are found only in ellipticals or recent merger events. We report B,R,J, and K imaging, optical spectroscopy, a rotation curve, an IRAS detection, and a VLA 20cm image for this galaxy, 0313-192. The optical and NIR images clearly show a disk. We detect apparent spiral arms and a dust-lane from B band imaging. The reddened nucleus is consistent with extinction by a similar dust-lane. The optical spectrum suggests a central AGN and some evidence of a starburst, with both the AGN and central starlight appearing substantially reddened. From analysis of the extended line emission in [OIII] and H-alpha we derive a rotation curve consistent with an early- type, dusty spiral seen edge-on. From the IRAS detection at 60 and 100 microns, we find that the ratio of Far IR to radio flux places this object firmly as a radio galaxy (i.e. the radio emission is not powered by star formation). The radio structure suggests that the radio source in this galaxy is related to the same physical mechanisms present in jet-fed powerful radio sources, and that such powerful, extended sources can (albeit extremely rarely) occur in a disk-dominated host.Comment: 30 pages LaTeX, 1 table, 8 postscript figures. Accepted for publication in the Astrophysical Journa

iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types.

Large-scale collections of induced pluripotent stem cells (iPSCs) could serve as powerful model systems for examining how genetic variation affects biology and disease. Here we describe the iPSCORE resource: a collection of systematically derived and characterized iPSC lines from 222 ethnically diverse individuals that allows for both familial and association-based genetic studies. iPSCORE lines are pluripotent with high genomic integrity (no or low numbers of somatic copy-number variants) as determined using high-throughput RNA-sequencing and genotyping arrays, respectively. Using iPSCs from a family of individuals, we show that iPSC-derived cardiomyocytes demonstrate gene expression patterns that cluster by genetic background, and can be used to examine variants associated with physiological and disease phenotypes. The iPSCORE collection contains representative individuals for risk and non-risk alleles for 95% of SNPs associated with human phenotypes through genome-wide association studies. Our study demonstrates the utility of iPSCORE for examining how genetic variants influence molecular and physiological traits in iPSCs and derived cell lines