Showing papers by "United States Geological Survey published in 2022"

Direct detection of RNA modifications and structure using single-molecule nanopore sequencing

Abstract: Modifications are present on many classes of RNA, including tRNA, rRNA, and mRNA. These modifications modulate diverse biological processes such as genetic recoding and mRNA export and folding. In addition, modifications can be introduced to RNA molecules using chemical probing strategies that reveal RNA structure and dynamics. Many methods exist to detect RNA modifications by short-read sequencing; however, limitations on read length inherent to short-read-based methods dissociate modifications from their native context, preventing single-molecule modification analysis. Here, we demonstrate direct RNA nanopore sequencing to detect endogenous and exogenous RNA modifications on long RNAs at the single-molecule level. We detect endogenous 2'-O-methyl and base modifications across E. coli and S. cerevisiae ribosomal RNAs as shifts in current signal and dwell times distally through interactions with the helicase motor protein. We further use the 2'-hydroxyl reactive SHAPE reagent acetylimidazole to probe RNA structure at the single-molecule level with readout by direct nanopore sequencing.

Modeling the Morphodynamics of Coastal Responses to Extreme Events: What Shape Are We In?

Abstract: This review focuses on recent advances in process-based numerical models of the impact of extreme storms on sandy coasts. Driven by larger-scale models of meteorology and hydrodynamics, these model...

Visually sensitive seizures: An updated review by the Epilepsy Foundation

Abstract: Light flashes, patterns, or color changes can provoke seizures in up to 1 in 4000 persons. Prevalence may be higher because of selection bias. The Epilepsy Foundation reviewed light-induced seizures in 2005. Since then, images on social media, virtual reality, three-dimensional (3D) movies, and the Internet have proliferated. Hundreds of studies have explored the mechanisms and presentations of photosensitive seizures, justifying an updated review. This literature summary derives from a nonsystematic literature review via PubMed using the terms “photosensitive” and “epilepsy.” The photoparoxysmal response (PPR) is an electroencephalography (EEG) phenomenon, and photosensitive seizures (PS) are seizures provoked by visual stimulation. Photosensitivity is more common in the young and in specific forms of generalized epilepsy. PS can coexist with spontaneous seizures. PS are hereditable and linked to recently identified genes. Brain imaging usually is normal, but special studies imaging white matter tracts demonstrate abnormal connectivity. Occipital cortex and connected regions are hyperexcitable in subjects with light-provoked seizures. Mechanisms remain unclear. Video games, social media clips, occasional movies, and natural stimuli can provoke PS. Virtual reality and 3D images so far appear benign unless they contain specific provocative content, for example, flashes. Images with flashes brighter than 20 candelas/m2 at 3-60 (particularly 15-20) Hz occupying at least 10 to 25% of the visual field are a risk, as are red color flashes or oscillating stripes. Equipment to assay for these characteristics is probably underutilized. Prevention of seizures includes avoiding provocative stimuli, covering one eye, wearing dark glasses, sitting at least two meters from screens, reducing contrast, and taking certain antiseizure drugs. Measurement of PPR suppression in a photosensitivity model can screen putative antiseizure drugs. Some countries regulate media to reduce risk. Visually-induced seizures remain significant public health hazards so they warrant ongoing scientific and regulatory efforts and public education.

Early life adversity has long-term effects on sociality and interaction style in female baboons

Abstract: Social bonds enhance fitness in many group-living animals, generating interest in the processes that create individual variation in sociality. Previous work on female baboons shows that early life adversity and temperament both influence social connectedness in adulthood. Early life adversity might shape sociality by reducing ability to invest in social relationships or through effects on attractiveness as a social partner. We examine how females’ early life adversity predicts sociality and temperament in wild olive baboons, and evaluate whether temperament mediates the relationship between early life adversity and sociality. We use behavioural data on 31 females to quantify sociality. We measure interaction style as the tendency to produce grunts (signals of benign intent) in contexts in which the vocalization does not produce immediate benefits to the actor. Early life adversity was negatively correlated with overall sociality, but was a stronger predictor of social behaviours received than behaviours initiated. Females who experienced less early life adversity had more benign interaction styles and benign interaction styles were associated with receiving more social behaviours. Interaction style may partially mediate the association between early life adversity and sociality. These analyses add to our growing understanding of the processes connecting early life experiences to adult sociality.

Tree Rings Reveal Unmatched 2nd Century Drought in the Colorado River Basin

Abstract: The ongoing 22-year drought in the Upper Colorado River Basin (UCRB) has been extremely severe, even in the context of the longest available tree-ring reconstruction of annual flow at Lees Ferry, Arizona, dating back to 762 CE. While many southwestern drought assessments have been limited to the past 1,200 years, longer paleorecords of moisture variability do exist for the UCRB. Here, gridded drought-atlas data in the UCRB domain along with naturalized streamflow data from the instrumental period (1906–2021) are used in a K-nearest neighbor nonparametric algorithm to develop a streamflow reconstruction for the Lees Ferry gage starting in 1 CE. The reconstruction reveals a second-century drought unmatched in severity by the current drought or by well-documented medieval period droughts in the UCRB. Although data are sparse, analysis of individual long tree-ring records and other paleoclimatic data also support the occurrence of an exceptional second-century drought.

Evaluating Microplastic Experimental Design and Exposure Studies in Aquatic Organisms

Abstract: Environmental microplastic particles (MPs) represent a potential threat to many aquatic animals, and experimental exposure studies, when done well, offer a quantitative approach to assess this stress systematically and reliably. While the scientific literature on MP studies in aquatic environments is rapidly growing, there is still much to learn, and this chapter presents a brief overview of some of the successful methods and pitfalls in experimental MP exposure studies. A short overview of some experimental design types and recommendations are also presented. A proper experimental exposure study will yield useful information on MP-organism impacts and must include the following: a comprehensive MP characterization (e.g., density, buoyancy, type, nature, size, shape, concentration, color, degree of weathering/biofilm formation, an assessment of co-contaminant/surfactant toxicity and behavior, an understanding exposure modes, dose and duration, and the type and life stage of the target species). Finally, more conventional experimental considerations, such as time, costs, and access to clean water, specialized instrumentation, and use of appropriate controls, replicate, and robust statistical analyses are also vital. This short review is intended as a necessary first step towards standardization of experimental MP exposure protocols so one can more reliably assess the transport and fate of MP in the aquatic environment as well as their potential impacts on aquatic organisms.

Earthquake‐Derived Seismic Velocity Changes During the 2018 Caldera Collapse of Kīlauea Volcano

Abstract: The 2018 Kīlauea caldera collapse produced extraordinary sequences of seismicity and deformation, with 62 episodic collapse events which significantly altered the landscape of the summit region. Despite decades of focused scientific studies at Kīlauea, detailed information about the internal structure of the volcano is limited. Recently developed techniques in seismic interferometry can be used to monitor the internal structure of an active volcano more directly by detecting subtle spatiotemporal changes in seismic wave velocity, but their utility relies on accurate interpretations of the underlying phenomena causing those velocity changes. Here, we retrospectively apply repeating-earthquake-based seismic interferometry to the 2018 Kīlauea eruption sequence. We find that seismic velocities changed over two distinct time scales: a sudden increase followed by a slower decrease in velocity in the hours following each collapse event, and a gradual, long-term decrease in velocity over several weeks that ceased approximately 1 month prior to the end of the eruption. Modeling suggests that short-term changes can be explained by magma reservoir pressurization which specifically closed vertical ring fractures. Long-term changes are related to subsidence of the caldera and likely include the influence of inelastic strain from the formation of new fractures. These observations provide new insights into the evolution of Kīlauea during its progressive collapse and will inform future interpretations for near-real-time monitoring at hazardous volcanoes around the world using similar techniques, especially where a dominant fracture orientation is present.

MIS 5e sea-level history along the Pacific coast of North America

Abstract: Abstract. The primary last interglacial, marine isotope substage (MIS) 5e records on the Pacific coast of North America, from Washington (USA) to Baja California Sur (Mexico), are found in the deposits of erosional marine terraces. Warmer coasts along the southern Golfo de California host both erosional marine terraces and constructional coral reef terraces. Because the northern part of the region is tectonically active, MIS 5e terrace elevations vary considerably, from a few meters above sea level to as much as 70 m above sea level. The primary paleo-sea-level indicator is the shoreline angle, the junction of the wave-cut platform with the former sea cliff, which forms very close to mean sea level. Most areas on the Pacific coast of North America have experienced uplift since MIS 5e time, but the rate of uplift varies substantially as a function of tectonic setting. Chronology in most places is based on uranium-series ages of the solitary coral Balanophyllia elegans (erosional terraces) or the colonial corals Porites and Pocillopora (constructional reefs). In areas lacking corals, correlation to MIS 5e often can be accomplished using amino acid ratios of fossil mollusks, compared to similar ratios in mollusks that also host dated corals. Uranium-series (U-series) analyses of corals that have experienced largely closed-system histories range from ∼124 to ∼118 ka, in good agreement with ages from MIS 5e reef terraces elsewhere in the world. There is no geomorphic, stratigraphic, or geochronological evidence for more than one high-sea stand during MIS 5e on the Pacific coast of North America. However, in areas of low uplift rate, the outer parts of MIS 5e terraces apparently were re-occupied by the high-sea stand at ∼100 ka (MIS 5c), evident from mixes of coral ages and mixes of molluscan faunas with differing thermal aspects. This sequence of events took place because glacial isostatic adjustment processes acting on North America resulted in regional high-sea stands at ∼100 and ∼80 ka that were higher than is the case in far-field regions, distant from large continental ice sheets. During MIS 5e time, sea surface temperatures (SSTs) off the Pacific coast of North America were higher than is the case at present, evident from extralimital southern species of mollusks found in dated deposits. Apparently, no wholesale shifts in faunal provinces took place, but in MIS 5e time, some species of bivalves and gastropods lived hundreds of kilometers north of their present northern limits, in good agreement with SST estimates derived from foraminiferal records and alkenone-based reconstructions in deep-sea cores. Because many areas of the Pacific coast of North America have been active tectonically for much or all of the Quaternary, many earlier interglacial periods are recorded as uplifted, higher-elevation terraces. In addition, from southern Oregon to northern Baja California, there are U-series-dated corals from marine terraces that formed at ∼80 ka, during MIS 5a. In contrast to MIS 5e, these terrace deposits host molluscan faunas that contain extralimital northern species, indicating cooler SST at the end of MIS 5. Here I present a review and standardized database of MIS 5e sea-level indicators along the Pacific coast of North America and the corresponding dated samples. The database is available in Muhs et al. (2021b; https://doi.org/10.5281/zenodo.5903285).

Multi‐Stage Soil‐Hydraulic Recovery and Limited Ravel Accumulations Following the 2017 Nuns and Tubbs Wildfires in Northern California

Abstract: Wildfire can impact soil-hydraulic properties by reducing saturated hydraulic conductivity and sorptivity, making recently burned landscapes prone to debris flows and flash floods. The post-fire hazard window can range from years to decades. In Northern California, where wildfire frequency is steadily increasing, the impact and soil-hydraulic recovery from wildfires is unknown. Following the October 2017 Nuns and Tubbs fires in the Northern Bay Area of California, we established 41 monitoring sites for repeat tension-disc infiltrometer measurements of field-saturated hydraulic conductivity (Kfs) over 3.5 years. Our site arrays, which encompass grasslands, chaparral, and oak and conifer forests across a range in lithology, show a marked decrease in Kfs following the wildfires and a swift partial recovery following the initial post-fire rainy season. Our time series reveals a complex path to soil-hydraulic recovery marked by distinct seasonal stages. Analysis of changing Kfs, sorptivity, and infiltration model residuals collectively suggests that these stages are related to transitions between soil-hydraulic processes like structural soil sealing from rainsplash, thermal cracking of bare soil, and vegetation regrowth. While soil infiltration rates were strongly impacted by the 2017 fires, dry ravel estimates are an order of magnitude less for similar slopes than the 2009 Station fire in the San Gabriel mountains of Southern California, suggesting that limited ravel flux may insufficiently load channels for debris flows that initiate from within-channel failure. Our analysis suggests that burned landscapes in the Northern Bay Area of California may experience rapid soil-hydraulic recovery and limited pathways toward post-fire debris flow initiation.

Mature Diffuse Tectonic Block Boundary Revealed by the 2020 Southwestern Puerto Rico Seismic Sequence

Abstract: Distributed faulting typically tends to coalesce into one or a few faults with repeated deformation. The progression of clustered medium-sized (≥Mw4.5) earthquakes during the 2020 seismic sequence in southwestern Puerto Rico (SWPR), modeling shoreline subsidence from InSAR, and sub-seafloor mapping by high-resolution seismic reflection profiles, suggest that the 2020 SWPR seismic sequence was distributed across several short intersecting strike-slip and normal faults beneath the insular shelf and upper slope of Guayanilla submarine canyon. Multibeam bathymetry map of the seafloor shows significant erosion and retreat of the shelf edge in the area of seismic activity as well as slope-parallel lineaments and submarine canyon meanders that typically develop over geological time. The T-axis of the moderate earthquakes further matches the extension direction previously measured on post early Pliocene (∼>3 Ma) faults. We conclude that although similar deformation has likely taken place in this area during recent geologic time, it does not appear to have coalesced during this time. The deformation may represent the southernmost part of a diffuse boundary, the Western Puerto Rico Deformation Boundary, which accommodates differential movement between the Puerto Rico and Hispaniola arc blocks. This differential movement is possibly driven by the differential seismic coupling along the Puerto Rico – Hispaniola subduction zone. We propose that the compositional heterogeneity across the island arc retards the process of focusing the deformation into a single fault. Given the evidence presented here, we should not expect a single large event in this area but similar diffuse sequences in the future. This article is protected by copyright. All rights reserved.

Seismic site characterization with shear wave (SH) reflection and refraction methods

Abstract: Abstract Reflection and critically refracted seismic methods use traveltime measurements of body waves propagating between a source and a series of receivers on the ground surface to calculate subsurface velocities. Body wave energy is refracted or reflected at boundaries where there is a change in seismic impedance, defined as the product of material density and seismic velocity. This article provides practical guidance on the use of horizontally propagating shear wave (SH-wave) refraction and reflection methods to determine shear wave velocity as a function of depth for near-surface seismic site characterizations. Method principles and the current state of engineering practice are reviewed, along with discussions of limitations and uncertainty assessments. Typical data collection procedures are described using basic survey equipment, along with information on more advanced applications and emerging technologies. Eight case studies provide examples of the techniques in real-world seismic site characterizations performed in a variety of geological settings.