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•We introduce software package RASP, which is a tool for historical biogeography.•We improve the widely used S-DIVA method, the DEC model, the Statistical DEC model and BayArea.•RASP ...also contains tools for combing the results from multiple runs and tools for removing widely distributed outgroups.
We announce the release of Reconstruct Ancestral State in Phylogenies (RASP), a user-friendly software package for inferring historical biogeography through reconstructing ancestral geographic distributions on phylogenetic trees. RASP utilizes the widely used Statistical-Dispersal Vicariance Analysis (S-DIVA), the Dispersal–Extinction–Cladogenesis (DEC) model (Lagrange), a Statistical DEC model (S-DEC) and BayArea. It provides a graphical user interface (GUI) to specify a phylogenetic tree or set of trees and geographic distribution constraints, draws pie charts on the nodes of a phylogenetic tree to indicate levels of uncertainty, and generates high-quality exportable graphical results. RASP can run on both Windows and Mac OS X platforms. All documentation and source code for RASP is freely available at http://mnh.scu.edu.cn/soft/blog/RASP.
•We describe the method of survey evaluation using re-detection ratio.•We present estimates of NEA population based on current survey completion.•We illustrate the utility of the method by ...investigating the population of “ARM-target” NEAs.
We describe a methodology of estimating the size–frequency distribution (SFD) of near-Earth asteroids (NEAs). We estimate the completion versus size of present surveys based on the re-detection ratio, that is, the fraction of all detections over a recent period that are re-detections of already discovered objects rather than new discoveries. The re-detection ratio is a robust measure of completion, but must be corrected for the obvious bias caused by differences in ease of discovery due to specific orbital geometries. We do this with a computer survey simulation using a large set of synthetic orbital elements matching as best possible the distribution of the real NEA population. Once suitably “calibrated” to match re-detections of the real survey, the completion estimate versus size derived from the simulation can be extended both to large size where few if any new detections are recorded, and to small sizes beyond where re-detection numbers are statistically significant, thereby providing an estimate of the population and survey completion over the entire range from the largest NEAs down to the smallest sizes detected (∼3m diameter). Here we update our previous population estimates and survey progress, using discoveries by surveys from August, 2012 through July, 2014. We estimate that there are 990±20 NEAs larger than 1km in diameter (absolute magnitude H⩽17.75), of which about 90% have been discovered as of August, 2014. We confirm a “dip” in the SFD, in the range from a few tens to a few hundreds of meters diameter, which may be due to the transition from larger “rubble pile” bodies to smaller “monolithic” bodies. We compare our population estimate at the smallest sizes with recent ones based on bolide frequency and find excellent agreement, within estimated errors. The same survey simulation methodology can be used to investigate population and survey completion of various subset populations, for example Earth-Crossing Asteroids (ECAs, with orbits crossing 1AU heliocentric distance), Potentially Hazardous Asteroids (PHAs, with orbits passing within 0.05AU of the Earth’s orbit), or Interior to Earth Asteroids (IEOs, with orbits entirely interior to the Earth’s orbit). Lastly, we have investigated the population and completion of so-called “ARM-target” asteroids, of size ∼10m diameter in orbits passing within 0.03AU of the Earth’s orbit with very low Earth-encounter velocity, <2.5km/s. We find current ground-based surveys are remarkably efficient in detecting this subset of NEAs, and are currently about 1% complete, implying a total population of such bodies of only a few thousand.
The intestinal microbiome is a unique ecosystem and an essential mediator of metabolism and obesity in mammals. However, studies investigating the impact of the diet on the establishment of the gut ...microbiome early in life are generally lacking, and most notably so in primate models. Here we report that a high-fat maternal or postnatal diet, but not obesity per se, structures the offspring's intestinal microbiome in Macaca fuscata (Japanese macaque). The resultant microbial dysbiosis is only partially corrected by a low-fat, control diet after weaning. Unexpectedly, early exposure to a high-fat diet diminished the abundance of non-pathogenic Campylobacter in the juvenile gut, suggesting a potential role for dietary fat in shaping commensal microbial communities in primates. Our data challenge the concept of an obesity-causing gut microbiome and rather provide evidence for a contribution of the maternal diet in establishing the microbiota, which in turn affects intestinal maintenance of metabolic health.
To assess the impact of genetic variation in regulatory loci on human health, we constructed a high-resolution map of allelic imbalances in DNA methylation, histone marks, and gene transcription in ...71 epigenomes from 36 distinct cell and tissue types from 13 donors. Deep whole-genome bisulfite sequencing of 49 methylomes revealed sequence-dependent CpG methylation imbalances at thousands of heterozygous regulatory loci. Such loci are enriched for stochastic switching, which is defined as random transitions between fully methylated and unmethylated states of DNA. The methylation imbalances at thousands of loci are explainable by different relative frequencies of the methylated and unmethylated states for the two alleles. Further analyses provided a unifying model that links sequence-dependent allelic imbalances of the epigenome, stochastic switching at gene regulatory loci, and disease-associated genetic variation.
ABSTRACT Knowledge of the surface thermal inertia of an asteroid can provide insight into its surface structure: porous material has a lower thermal inertia than rock. We develop a means to estimate ...thermal inertia values of asteroids and use it to show that thermal inertia appears to increase with spin period in the case of main-belt asteroids (MBAs). Similar behavior is found on the basis of thermophysical modeling for near-Earth objects (NEOs). We interpret our results in terms of rapidly increasing material density and thermal conductivity with depth, and provide evidence that thermal inertia increases by factors of 10 (MBAs) to 20 (NEOs) within a depth of just 10 cm. Our results are consistent with a very general picture of rapidly changing material properties in the topmost regolith layers of asteroids and have important implications for calculations of the Yarkovsky effect, including its perturbation of the orbits of potentially hazardous objects and those of asteroid family members after the break-up event. Evidence of a rapid increase of thermal inertia with depth is also an important result for studies of the ejecta-enhanced momentum transfer of impacting vehicles ("kinetic impactors") in planetary defense.
The axon initial segment (AIS) is a critical locus of control of action potential (AP) generation and neuronal information synthesis. Concussive traumatic brain injury gives rise to diffuse axotomy, ...and the majority of neocortical axonal injury arises at the AIS. Consequently, concussive traumatic brain injury might profoundly disrupt the functional specialization of this region. To investigate this hypothesis, one and two days after mild central fluid percussion injury in Thy1-YFP-H mice, we recorded high-resolution APs from axotomized and adjacent intact layer 5 pyramidal neurons and applied a second derivative (2
) analysis to measure the AIS- and soma-regional contributions to the AP upstroke. All layer 5 pyramidal neurons recorded from sham animals manifested two stark 2
peaks separated by a negative intervening slope. In contrast, within injured mice, we discovered a subset of axotomized layer 5 pyramidal neurons in which the AIS-regional 2
peak was abolished, a functional perturbation associated with diminished excitability, axonal sprouting and distention of the AIS as assessed by staining for ankyrin-G. Our analysis revealed an additional subpopulation of both axotomized and intact layer 5 pyramidal neurons that manifested a melding together of the AIS- and soma-regional 2
peaks, suggesting a more subtle aberration of sodium channel function and/or translocation of the AIS initiation zone closer to the soma. When these experiments were repeated in animals in which cyclophilin-D was knocked out, these effects were ameliorated, suggesting that trauma-induced AIS functional perturbation is associated with mitochondrial calcium dysregulation.
Our understanding of the evolutionary history of primates is undergoing continual revision due to ongoing genome sequencing efforts. Bolstered by growing fossil evidence, these data have led to ...increased acceptance of once controversial hypotheses regarding phylogenetic relationships, hybridization and introgression, and the biogeographical history of primate groups. Among these findings is a pattern of recent introgression between species within all major primate groups examined to date, though little is known about introgression deeper in time. To address this and other phylogenetic questions, here, we present new reference genome assemblies for 3 Old World monkey (OWM) species: Colobus angolensis ssp. palliatus (the black and white colobus), Macaca nemestrina (southern pig-tailed macaque), and Mandrillus leucophaeus (the drill). We combine these data with 23 additional primate genomes to estimate both the species tree and individual gene trees using thousands of loci. While our species tree is largely consistent with previous phylogenetic hypotheses, the gene trees reveal high levels of genealogical discordance associated with multiple primate radiations. We use strongly asymmetric patterns of gene tree discordance around specific branches to identify multiple instances of introgression between ancestral primate lineages. In addition, we exploit recent fossil evidence to perform fossil-calibrated molecular dating analyses across the tree. Taken together, our genome-wide data help to resolve multiple contentious sets of relationships among primates, while also providing insight into the biological processes and technical artifacts that led to the disagreements in the first place.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Preterm birth (PTB) is a leading cause of neonatal morbidity and mortality and is not uncommonly associated with chorioamnionitis. We recently have demonstrated that the placenta harbors a unique ...microbiome with similar flora to the oral community. We also have shown an association of these placental microbiota with PTB, history of antenatal infection, and excess maternal weight gain. On the basis of these previous observations, we hypothesized that the placental membranes would retain a microbiome community that would vary in association with preterm birth and chorioamnionitis.
In the current study, we aimed to examine the differences in the placental membrane microbiome in association with PTB in both the presence and absence of chorioamnionitis and/or funisitis using state-of-the-science whole-genome shotgun metagenomics.
This was a cross-sectional analysis with 6 nested spontaneous birth cohorts (n = 9−15 subjects/cohort): Term gestations without chorioamnionitis, term with chorioamnionitis, preterm without chorioamnionitis, preterm with mild chorioamnionitis, preterm with severe chorioamnionitis, and preterm with chorioamnionitis and funisitis. Histologic analysis was performed with Redline’s criteria, and inflammatory cytokines were analyzed in the cord blood. DNA from placental membranes was extracted from sterile swabs collected at delivery, and whole-genome shotgun sequencing was performed on the Illumina HiSeq platform. Filtered microbial DNA sequences were annotated and analyzed with MG-RAST (ie, Metagenomic Rapid Annotations using Subsystems Technology) and R.
Subjects were assigned to cohorts on the basis of gestational age at delivery and independent scoring of histologic chorioamnionitis. We found that preterm subjects with severe chorioamnionitis and funisitis had increases in cord blood inflammatory cytokines. Of interest, although the placental membrane microbiome was altered in association with severity of histologic chorioamnionitis (permutational multivariate analysis of variance P = .005), there was no observable impact with either betamethasone or antibiotic treatment. In preterm subjects with chorioamnionitis, we found a high abundance of both urogenital and oral commensal bacteria. These alterations in the microbiome were accompanied by significant variation (P < .05) in microbial metabolic pathways important in the glucose-fed pentose phosphate pathway (term subjects), or glycerophopholipid metabolism, and the biosynthesis of the siderophore group nonribosomal peptides (preterm subjects).
Consistent with ours and others previous findings, women who experienced spontaneous PTB harbor placental microbiota that further differed by severity of chorioamnionitis. Integrative metagenomic analysis revealed significant variation in distinct bacterial metabolic pathways, which we speculate may contribute to risk of preterm birth with and without severe chorioamnionitis.
The thermal inertia of an asteroid's surface can provide insight into regolith properties, such as the presence of a layer of fine dust, the density and thermal conductivity of a rocky surface, and, ...together with other observational data, mineralogy. Knowledge of the surface characteristics of asteroids is important for planetary defense initiatives and the extraction of resources ("asteroid mining"). A simple means of estimating asteroid thermal inertia has been proposed by Harris & Drube, which is suitable for application to large sets of thermal-infrared observational data, such as those obtained by infrared space telescopes. We compare results from the Harris-Drube estimator with recently published values of asteroid thermal inertia from detailed thermophysical modeling, and provide an explanation in terms of reduced surface roughness for some discrepant results. Smooth surfaces covered in fine dust may provide an explanation for the unexpectedly low values of thermal inertia derived from thermophysical modeling for some slowly rotating main-belt asteroids. In the case of near-Earth objects (NEOs) we show that results from the estimator are in good agreement with those from thermophysical modeling, with just a few exceptions. We discuss the special cases of the NEOs (101955) Bennu, (162173) Ryugu, and (29075) 1950 DA in the context of results from our estimator. Given the data requirements and complexity of thermophysical modeling, data-analysis tools based on relatively simple concepts can play an important role in allowing "quick-look" assessment of thermal-infrared data of asteroids, especially NEOs.
While breast milk has unique health advantages for infants, the mechanisms by which it regulates the physiology of newborns are incompletely understood. miRNAs have been described as functioning ...transcellularly, and have been previously isolated in cell-free and exosomal form from bodily liquids (serum, saliva, urine) and tissues, including mammary tissue. We hypothesized that breast milk in general, and milk fat globules in particular, contain significant numbers of known and limited novel miRNA species detectable with massively parallel sequencing. Extracted RNA from lactating mothers before and following short-term treatment with recombinant human growth hormone (rhGH) was smRNA-enriched. smRNA-Seq was performed to generate 124,110,646 36-nt reads. Of these, 31,102,927 (25%) exactly matched known human miRNAs; with relaxing of stringency, 74,716,151 (60%) matched known miRNAs including 308 of the 1018 (29%) mature miRNAs (miRBase 16.0). These miRNAs are predicted to target 9074 genes; the 10 most abundant of these predicted to target 2691 genes with enrichment for transcriptional regulation of metabolic and immune responses. We identified 21 putative novel miRNAs, of which 12 were confirmed in a large validation set that included cohorts of lactating women consuming enriched diets. Of particular interest, we observed that expression of several novel miRNAs were altered by the perturbed maternal diet, notably following a high-fat intake (p<0.05). Our findings suggest that known and novel miRNAs are enriched in breast milk fat globules, and expression of several novel miRNA species is regulated by maternal diet. Based on robust pathway mapping, our data supports the notion that these maternally secreted miRNAs (stable in the milk fat globules) play a regulatory role in the infant and account in part for the health benefits of breast milk. We further speculate that regulation of these miRNA by a high fat maternal diet enables modulation of fetal metabolism to accommodate significant dietary challenges.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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