Ray-finned fishes make up half of all living vertebrate species. Nearly all ray-finned fishes are teleosts, which include most commercially important fish species, several model organisms for ...genomics and developmental biology, and the dominant component of marine and freshwater vertebrate faunas. Despite the economic and scientific importance of ray-finned fishes, the lack of a single comprehensive phylogeny with corresponding divergence-time estimates has limited our understanding of the evolution and diversification of this radiation. Our analyses, which use multiple nuclear gene sequences in conjunction with 36 fossil age constraints, result in a well-supported phylogeny of all major rayfinned fish lineages and molecular age estimates that are generally consistent with the fossil record. This phylogeny informs three longstanding problems: specifically identifying elopomorphs (eels and tarpons) as the sister lineage of all other teleosts, providing a unique hypothesis on the radiation of early euteleosts, and offering a promising strategy for resolution of the "bush at the top of the tree" that includes percomorphs and other spiny-finned teleosts. Contrasting our divergence time estimates with studies using a single nuclear gene or whole mitochondrial genomes, we find that the former underestimates ages of the oldest ray-finned fish divergences, but the latter dramatically overestimates ages for derived teleost lineages. Our time-calibrated phylogeny reveals that much of the diversification leading to extant groups of teleosts occurred between the late Mesozoic and early Cenozoic, identifying this period as the "Second Age of Fishes."
Alzheimer's disease (AD) causes unrelenting, progressive cognitive impairments, but its course is heterogeneous, with a broad range of rates of cognitive decline
. The spread of tau aggregates ...(neurofibrillary tangles) across the cerebral cortex parallels symptom severity
. We hypothesized that the kinetics of tau spread may vary if the properties of the propagating tau proteins vary across individuals. We carried out biochemical, biophysical, MS and both cell- and animal-based-bioactivity assays to characterize tau in 32 patients with AD. We found striking patient-to-patient heterogeneity in the hyperphosphorylated species of soluble, oligomeric, seed-competent tau. Tau seeding activity correlates with the aggressiveness of the clinical disease, and some post-translational modification (PTM) sites appear to be associated with both enhanced seeding activity and worse clinical outcomes, whereas others are not. These data suggest that different individuals with 'typical' AD may have distinct biochemical features of tau. These data are consistent with the possibility that individuals with AD, much like people with cancer, may have multiple molecular drivers of an otherwise common phenotype, and emphasize the potential for personalized therapeutic approaches for slowing clinical progression of AD.
Drylands make up roughly 40% of the Earth's land surface, and billions of people depend on services provided by these critically important ecosystems. Despite their relatively sparse vegetation, ...dryland ecosystems are structurally and functionally diverse, and emerging evidence suggests that these ecosystems play a dominant role in the trend and variability of the terrestrial carbon sink. More, drylands are highly sensitive to climate and are likely to have large, non-linear responses to hydroclimatic change. Monitoring the spatiotemporal dynamics of dryland ecosystem structure (e.g., leaf area index) and function (e.g., primary production and evapotranspiration) is therefore a high research priority. Yet, dryland remote sensing is defined by unique challenges not typically encountered in mesic or humid regions. Major challenges include low vegetation signal-to-noise ratios, high soil background reflectance, presence of photosynthetic soils (i.e., biological soil crusts), high spatial heterogeneity from plot to regional scales, and irregular growing seasons due to unpredictable seasonal rainfall and frequent periods of drought. Additionally, there is a relative paucity of continuous, long-term measurements in drylands, which impedes robust calibration and evaluation of remotely-sensed dryland data products. Due to these issues, remote sensing techniques developed in other ecosystems or for global application often result in inaccurate, poorly constrained estimates of dryland ecosystem structural and functional dynamics. Here, we review past achievements and current progress in remote sensing of dryland ecosystems, including a detailed discussion of the major challenges associated with remote sensing of key dryland structural and functional dynamics. We then identify strategies aimed at leveraging new and emerging opportunities in remote sensing to overcome previous challenges and more accurately contextualize drylands within the broader Earth system. Specifically, we recommend: 1) Exploring novel combinations of sensors and techniques (e.g., solar-induced fluorescence, thermal, microwave, hyperspectral, and LiDAR) across a range of spatiotemporal scales to gain new insights into dryland structural and functional dynamics; 2) utilizing near-continuous observations from new-and-improved geostationary satellites to capture the rapid responses of dryland ecosystems to diurnal variation in water stress; 3) expanding ground observational networks to better represent the heterogeneity of dryland systems and enable robust calibration and evaluation; 4) developing algorithms that are specifically tuned to dryland ecosystems by utilizing expanded ground observational network data; and 5) coupling remote sensing observations with process-based models using data assimilation to improve mechanistic understanding of dryland ecosystem dynamics and to better constrain ecological forecasts and long-term projections.
•We highlight major historical milestones in dryland remote sensing.•Drylands have historically been important regions for remote sensing innovation.•Drylands, in turn, have emerged as key drivers of variability in land CO2 uptake.•Dryland remote sensing faces unique challenges not encountered in many ecosystems.•We recommend new assets and techniques as a path forward for dryland remote sensing.
By decomposing genome sequences into k-mers, it is possible to estimate genome differences without alignment. Techniques such as k-mer minimisers, for example MinHash, have been developed and are ...often accurate approximations of distances based on full k-mer sets. These and other alignment-free methods avoid the large temporal and computational expense of alignment. However, these k-mer set comparisons are not entirely accurate within-species and can be completely inaccurate within-lineage. This is due, in part, to their inability to distinguish core polymorphism from accessory differences. Here we present a new approach, KmerAperture, which uses information on the k-mer relative genomic positions to determine the type of polymorphism causing differences in k-mer presence and absence between pairs of genomes. Single SNPs are expected to result in k unique contiguous k-mers per genome. On the other hand, contiguous series > k may be caused by accessory differences of length S-k+1; when the start and end of the sequence are contiguous with homologous sequence. Alternatively, they may be caused by multiple SNPs within k bp from each other and KmerAperture can determine whether that is the case. To demonstrate use cases KmerAperture was benchmarked using datasets including a very low diversity simulated population with accessory content independent from the number of SNPs, a simulated population where SNPs are spatially dense, a moderately diverse real cluster of genomes (Escherichia coli ST1193) with a large accessory genome and a low diversity real genome cluster (Salmonella Typhimurium ST34). We show that KmerAperture can accurately distinguish both core and accessory sequence diversity without alignment, outperforming other k-mer based tools.
Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using ...long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.
Malaria mosquitoes acoustically detect their mating partners within large swarms that form transiently at dusk. Indeed, male malaria mosquitoes preferably respond to female flight tones during swarm ...time. This phenomenon implies a sophisticated context- and time-dependent modulation of mosquito audition, the mechanisms of which are largely unknown. Using transcriptomics, we identify a complex network of candidate neuromodulators regulating mosquito hearing in the species Anopheles gambiae. Among them, octopamine stands out as an auditory modulator during swarm time. In-depth analysis of octopamine auditory function shows that it affects the mosquito ear on multiple levels: it modulates the tuning and stiffness of the flagellar sound receiver and controls the erection of antennal fibrillae. We show that two α- and β-adrenergic-like octopamine receptors drive octopamine's auditory roles and demonstrate that the octopaminergic auditory control system can be targeted by insecticides. Our findings highlight octopamine as key for mosquito hearing and mating partner detection and as a potential novel target for mosquito control.
The clinical progression of Alzheimer disease (AD) is associated with the accumulation of tau neurofibrillary tangles, which may spread throughout the cortex by interneuronal tau transfer. If so, ...targeting extracellular tau species may slow the spreading of tau pathology and possibly cognitive decline. To identify suitable target epitopes, we tested the effects of a panel of tau antibodies on neuronal uptake and aggregation in vitro. Immunodepletion was performed on brain extract from tau-transgenic mice and postmortem AD brain and added to a sensitive fluorescence resonance energy transfer–based tau uptake assay to assess blocking efficacy. The antibodies reduced tau uptake in an epitope-dependent manner: N-terminal (Tau13) and middomain (6C5 and HT7) antibodies successfully prevented uptake of tau species, whereas the distal C-terminal–specific antibody (Tau46) had little effect. Phosphorylation-dependent (40E8 and p396) and C-terminal half (4E4) tau antibodies also reduced tau uptake despite removing less total tau by immunodepletion, suggesting specific interactions with species involved in uptake. Among the seven antibodies evaluated, 6C5 most efficiently blocked uptake and subsequent aggregation. More important, 6C5 also blocked neuron-to-neuron spreading of tau in a unique three-chamber microfluidic device. Furthermore, 6C5 slowed down the progression of tau aggregation even after uptake had begun. Our results imply that not all antibodies/epitopes are equally robust in terms of blocking tau uptake of human AD-derived tau species.
Since the discovery of scarless fetal skin wound healing, research in the field has expanded significantly with the hopes of advancing the finding to adult human patients. There are several ...differences between fetal and adult skin that have been exploited to facilitate scarless healing in adults including growth factors, cytokines, and extracellular matrix substitutes. However, no one therapy, pathway, or cell subtype is sufficient to support scarless wound healing in adult skin. More recently, products that contain or mimic fetal and adult uninjured dermis were introduced to the wound healing market with promising clinical outcomes. Through our review of the major experimental targets of fetal wound healing, we hope to encourage research in areas that may have a significant clinical impact. Additionally, we will investigate therapies currently in clinical use and evaluate whether they represent a legitimate advance in regenerative medicine or a vulnerary agent. WIREs Dev Biol 2018, 7:e309. doi: 10.1002/wdev.309 This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Plant Development > Cell Growth and Differentiation Adult Stem Cells, Tissue Renewal, and Regeneration > Environmental Control of Stem Cells.
There have been increasing attempts to reverse habitat degradation through active restoration, but few large-scale successes are reported to guide these efforts. Here, we report outcomes from a ...unique and very successful seagrass restoration project: Since 1999, over 70 million seeds of a marine angiosperm, eelgrass (
), have been broadcast into mid-western Atlantic coastal lagoons, leading to recovery of 3612 ha of seagrass. Well-developed meadows now foster productive and diverse animal communities, sequester substantial stocks of carbon and nitrogen, and have prompted a parallel restoration for bay scallops (
Restored ecosystem services are approaching historic levels, but we also note that managers value services differently today than they did nine decades ago, emphasizing regulating in addition to provisioning services. Thus, this study serves as a blueprint for restoring and maintaining healthy ecosystems to safeguard multiple benefits, including co-benefits that may emerge as management priorities over time.
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