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Rupturing of the primary fault may trigger secondary fault activity in a complex multi-fault system. The mainshock focal mechanism and well-constrained aftershock locations reveal vital information about aftershock migration patterns, the regional tectonic stress field, and the seismogenic process. Aftershock relocations of the events in the Utah Mw5.7 earthquake sequence that occurred on March 18, 2020, indicate that the mainshock ruptured a listric normal fault; this fault is characterized by a shallow concave upward fault surface and a dip that decreases with depth. The aftershocks were largely organized into two clusters. The first small cluster, which is located ~ 8 km east of the mainshock, resides on part of a fault that is steeply dipping to the east; the second larger cluster is spread across multiple conjugate faults. Using local and regional waveforms to estimate the seismic moment tensor solutions, we determined that the Utah MW5.7 mainshock was a shallow crustal normal faulting event. Furthermore, 11 selected aftershocks (MW ≥ 3.3) are also characterized by normal faulting. The nearly EW-oriented extensional stress pattern in the focal area has an orientation that is similar to that of the regional maximum horizontal extensional stress field. Our analysis of the Coulomb stress variations showed that the Utah Mw5.7 earthquake triggered the aftershocks that formed along conjugate normal faults near the West Valley fault zone. These results provide evidence for the triggering hypothesis, wherein subsequent seismic events are caused by static stress changes triggered by large mainshock earthquakes. [ABSTRACT FROM AUTHOR]

The conserved shelterin complex caps chromosome ends to protect telomeres and regulate telomere replication. In fission yeast Schizosaccharomyces pombe, shelterin consists of telomeric single- and double-stranded DNA-binding modules Pot1-Tpz1 and Taz1-Rap1 connected by Poz1, and a specific component Ccq1. While individual structures of the two DNA-binding OB folds of Pot1 (Pot1OB1-GGTTAC and Pot1OB2-GGTTACGGT) are available, structural insight into recognition of telomeric repeats with spacers by the complete DNA-binding domain (Pot1DBD) remains an open question. Moreover, structural information about the Tpz1-Ccq1 interaction requires to be revealed for understanding how the specific component Ccq1 of S. pombe shelterin is recruited to telomeres to function as an interacting hub. Here, we report the crystal structures of Pot1DBD-single-stranded-DNA, Pot1372-555-Tpz1185-212 and Tpz1425-470-Ccq1123-439 complexes and propose an integrated model depicting the assembly mechanism of the shelterin complex at telomeres. The structure of Pot1DBD-DNA unveils how Pot1 recognizes S. pombe degenerate telomeric sequences. Our analyses of Tpz1-Ccq1 reveal structural basis for the essential role of the Tpz1-Ccq1 interaction in telomere recruitment of Ccq1 that is required for telomere maintenance and telomeric heterochromatin formation. Overall, our findings provide valuable structural information regarding interactions within fission yeast shelterin complex at 3' ss telomeric overhang. Author summary: Telomeres, composed of repetitive DNA sequences and specialized proteins, are protective structures at the ends of linear chromosomes. The telomere structure is essential for the maintenance of genome integrity and stability, and telomere dysfunction has been linked to human development, aging, cancer and a variety of degenerative diseases. An evolutionarily conserved multiple-protein complex called shelterin plays versatile roles in telomere homeostasis regulation, end protection and heterochromatin establishment. However, the highly flexible nature of shelterin complex has greatly impeded our structural and functional understanding for this important complex. In fission yeast, structures of the shelterin dsDNA-binding protein subcomplex Taz1-Rap1 and the bridge subcomplex Tpz1-Poz1-Rap1 are available. Although individual OB-fold subdomains structures have been characterized, structural information about the complete Pot1DBD bound to telomeric repeats with spacers remains to be revealed. Here, by determining the crystal structures of the telomeric overhang binding Pot1DBD-ssDNA, Pot1372-555-Tpz1185-212 and Tpz1425-470-Ccq1123-439 subcomplexes, we provide structural basis not only for the recognition of S. pombe degenerate telomeric sequences by Pot1, but also for the essential function of the Tpz1-Ccq1 interaction in Ccq1 recruitment to telomeres for telomere maintenance and telomeric heterochromatin formation. These findings provide an integrated model depicting the assembly mechanism of the shelterin complex at telomeres and its multiple roles in telomere biology. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 and its variants, such as the Omicron continue to threaten public health. The virus recognizes the host cell by attaching its Spike (S) receptor-binding domain (RBD) to the host receptor, ACE2. Therefore, RBD is a primary target for neutralizing antibodies and vaccines. Here, we report the isolation and biological and structural characterization of a single-chain antibody (nanobody) from RBD-immunized alpaca. The nanobody, named DL28, binds to RBD tightly with a K D of 1.56 nM and neutralizes the original SARS-CoV-2 strain with an IC50 of 0.41 μg mL−1. Neutralization assays with a panel of variants of concern (VOCs) reveal its wide-spectrum activity with IC50 values ranging from 0.35 to 1.66 μg mL−1 for the Alpha/Beta/Gamma/Delta and an IC50 of 0.66 μg mL−1 for the currently prevalent Omicron. Competition binding assays show that DL28 blocks ACE2-binding. However, structural characterizations and mutagenesis suggest that unlike most antibodies, the blockage by DL28 does not involve direct competition or steric hindrance. Rather, DL28 may use a "conformation competition" mechanism where it excludes ACE2 by keeping an RBD loop in a conformation incompatible with ACE2-binding. [ABSTRACT FROM AUTHOR]

Deep subduction of plate generally could induce a partial molten low‐velocity layer (LVL) atop the mantle transition zone (MTZ) around the subduction zone. But the effects of the LVL to its upper lithosphere are less known, especially at the oceanward direction of subducted slab. Here, we image the seismic velocity structure atop the MTZ by matching the synthetics and the observed triplicated P‐ and SH‐wave waveforms recorded by Xinjiang seismic network from four earthquakes in the southwestern Siberia. Our observations reveal a partial molten LVL atop the MTZ beneath the western Junggar (WJ) in the southwestern Central Asian Orogenic Belt. The SH‐wave velocity drop for the LVL is −5.6% which is larger than −4.4% of the P‐wave when its thickness is 29 km. It is inferred that the subducted Paleo‐Asian oceanic plate induces hydrous MTZ materials underneath the subducted slab to upwell to the upper mantle, and form the partial molten LVL. Combined with previous geophysical and geological results, we propose a new geodynamical process involving the lithosphere and MTZ underneath the subducted slab: the melt in the LVL is likely to upwell through slab window, which could be triggered by mid‐oceanic ridge subduction or self‐sustained buoyancy. This mode could account for the contemporaneous break‐off fossil oceanic plate, ocean island basalts‐type rocks, extensive A‐type granitoids, adakite, and porphyry Cu‐Au in the WJ during the late Carboniferous to early Permian. Plain Language Summary: Different types of rocks indicate a mantle plume or enriched asthenospheric mantle upwelling in the western Junggar (WJ) during the late Carboniferous to early Permian. However, the related magma origin is not clear. Through matching the synthetics and the observed triplicated P‐ and SH‐wave waveforms, we detect a partial molten low‐velocity layer (LVL) atop the mantle transition zone (MTZ) beneath the WJ in northwestern Xinjiang, China. We infer that the formation of the LVL is related to the subduction of the Paleo‐Asian oceanic plate. The LVL may be the origin of a mantle plume flowing upward through slab window, which could help to explain the formation of break‐off fossil oceanic plate and various rocks, such as ocean island basalts‐type rocks, extensive A‐type granitoids, adakite, and porphyry Cu‐Au. Key Points: We explore P and SH velocities around depth of 410 km by triplicated waveform modelingA partial molten low‐velocity layer (LVL) is found atop the mantle transition zone in the western JunggarThe LVL may be a mantle plume origin induced by the ancient subducted plate [ABSTRACT FROM AUTHOR]

The Qiangtang terrane exhibits many unique features compared with surrounding areas in the Tibetan plateau. It has been largely remodeled by the northward downwelling of the Indian lithosphere and the vertical upwelling of the Eurasian asthenosphere. Here, we investigate the P‐wave velocity around the mantle transition zone (MTZ) beneath the Qiangtang terrane using high‐frequency triplicated waveforms recorded by the China Digital Seismic Network. We found a low‐velocity layer (LVL) atop the MTZ and a high‐velocity anomaly (HVA) in the lower part of the MTZ. They are characterized by thickness of 36 km with velocity drop of −2.0% and 155 km with velocity increment of 1.2%, respectively. The 410 and 660 km discontinuities are depressed by different depths of 12 and 30 km, suggesting a thickened MTZ. In combination with previous multi‐disciplinary observations, we infer that the LVL is a hydrous partial melt affected by dehydration and high temperature, and the HVA is due to water and low temperature conditions. The downwelling cold continental lithosphere may have accumulated in the lower MTZ and induced the hydrous hot MTZ materials to upwelling until the shallow depths of the upper mantle beneath the Qiangtang terrane. Plain Language Summary: The Qiangtang terrane is located in front of the northward downwelling Indian plate. Whether there are material exchanges between the upper mantle and the mantle transition zone (MTZ) is on debate. Our observations of P‐wave triplicated waveforms reveal a low‐velocity layer atop the MTZ and a high‐velocity anomaly in the lower MTZ. Different scales of depressed 410 and 660 km discontinuities suggest a thickened MTZ. We suggest a dynamic model of mantle convection involving the asthenosphere and the MTZ for the evolution of the Tibetan plateau. Key Points: Triplicated waveform modeling is used to constrain velocity variation around the mantle transition zone (MTZ)Low‐ and high‐velocity anomalies are found atop and at the bottom of the MTZ beneath the Qiangtang terranceThere is an upwelling of the hydrous MTZ materials in front of the downwelling continental lithosphere [ABSTRACT FROM AUTHOR]

Background: Analysis of viral protein–protein interactions is an essential step to uncover the viral protein functions and the molecular mechanism for the assembly of a viral protein complex. We employed a mammalian two-hybrid system to screen all the viral proteins of SARS-CoV-2 for the protein–protein interactions. Results: Our study detected 48 interactions, 14 of which were firstly reported here. Unlike Nsp1 of SARS-CoV, Nsp1 of SARS-CoV-2 has the most interacting partners among all the viral proteins and likely functions as a hub for the viral proteins. Five self-interactions were confirmed, and five interactions, Nsp1/Nsp3.1, Nsp3.1/N, Nsp3.2/Nsp12, Nsp10/Nsp14, and Nsp10/Nsp16, were determined to be positive bidirectionally. Using the replicon reporter system of SARS-CoV-2, we screened all viral Nsps for their impacts on the viral replication and revealed Nsp3.1, the N-terminus of Nsp3, significantly inhibited the replicon reporter gene expression. We found Nsp3 interacted with N through its acidic region at N-terminus, while N interacted with Nsp3 through its NTD, which is rich in the basic amino acids. Furthermore, using purified truncated N and Nsp3 proteins, we determined the direct interactions between Nsp3 and N protein. Conclusions: Our findings provided a basis for understanding the functions of coronavirus proteins and supported the potential of interactions as the target for antiviral drug development. [ABSTRACT FROM AUTHOR]

Serotonin N‐acetyltransferase (SNAT) is the key rate‐limiting enzyme in melatonin biosynthesis. It mediates melatonin biosynthesis in plants by using serotonin and 5‐methoxytryptamine (5‐MT), but little is known of its underlying mechanisms. Herein, we present a detailed reaction mechanism of a SNAT from Oryza sativa through combined structural and molecular dynamics (MD) analysis. We report the crystal structures of plant SNAT in the apo and binary/ternary complex forms with acetyl‐CoA (AcCoA), serotonin, and 5‐MT. OsSNAT exhibits a unique enzymatically active dimeric fold not found in the known structures of arylalkylamine N‐acetyltransferase (AANAT) family. The key residues W188, D189, D226, N220, and Y233 located around the active pocket are important in catalysis, confirmed by site‐directed mutagenesis. Combined with MD simulations, we hypothesize a novel plausible catalytic mechanism in which D226 and Y233 function as catalytic base and acid during the acetyl‐transfer reaction. [ABSTRACT FROM AUTHOR]

Serotonin N‐acetyltransferase (SNAT) is the key rate‐limiting enzyme in melatonin biosynthesis. It mediates melatonin biosynthesis in plants by using serotonin and 5‐methoxytryptamine (5‐MT), but little is known of its underlying mechanisms. Herein, we present a detailed reaction mechanism of a SNAT from Oryza sativa through combined structural and molecular dynamics (MD) analysis. We report the crystal structures of plant SNAT in the apo and binary/ternary complex forms with acetyl‐CoA (AcCoA), serotonin, and 5‐MT. OsSNAT exhibits a unique enzymatically active dimeric fold not found in the known structures of arylalkylamine N‐acetyltransferase (AANAT) family. The key residues W188, D189, D226, N220, and Y233 located around the active pocket are important in catalysis, confirmed by site‐directed mutagenesis. Combined with MD simulations, we hypothesize a novel plausible catalytic mechanism in which D226 and Y233 function as catalytic base and acid during the acetyl‐transfer reaction. [ABSTRACT FROM AUTHOR]

S‐adenosyl‐L‐methionine (SAM)‐dependent methyltransferases (MTases) are widely distributed among almost all organisms and often characterized with conserved Rossmann fold, TIM barrel, and D×G×G×G motif. However, some MTases show no methyltransferase activity. In the present study, the crystal structure of LepI, one MTase‐like enzyme isolated from A. flavus that catalyzes pericyclic reactions, was investigated to determine its structure‐function relationship. The overall structure of LepI in complex with the SAM mimic S‐adenosyl‐L‐homocysteine (SAH) (PDB ID: 6IV7) indicated that LepI is a tetramer in solution. The residues His133, Arg197, Arg295, and Asp296 located near the active site can form hydrogen bonds with the substrate, thus participating in catalytic reactions. The binding of SAH in LepI is almost identical to that in other resolved MTases; however, the location of catalytic residues differs significantly. Phylogenetic trials suggest that LepI proteins share a common ancestor in plants and algae, which may explain the conserved SAM‐binding site. However, the accelerated evolution of A. flavus has introduced both functional and structural changes in LepI. More importantly, the residue Arg295, which is unique to LepI, might be a key determinant for the altered enzymatic behavior. Collectively, the differences in the composition of catalytic residues, as well as the unique tetrameric form of LepI, define its unique enzymatic behavior. The present work provides an additional understanding of the structure‐function relationship of MTases and MTase‐like enzymes. [ABSTRACT FROM AUTHOR]

Summary: Despite of important functions of strigolactones (SLs) and karrikins (KARs) in plant development, plant–parasite and plant–fungi interactions, their roles in soybean–rhizobia interaction remain elusive. SL/KAR signaling genes GmMAX2a, GmD14s, and GmKAIs are activated by rhizobia infection. GmMAX2a restored atmax2 root hair defects and soybean root hairs were changed in GmMAX2a overexpression (GmMAX2a‐OE) or knockdown (GmMAX2a‐KD) mutants. GmMAX2a‐KD gave fewer, whereas GmMAX2a‐OE produced more nodules than GUS hairy roots. Mutation of GmMAX2a in its KD or OE transgenic hairy roots affected the rhizobia infection‐induced increases in early nodulation gene expression. Both mutant hairy roots also displayed the altered auxin, jasmonate and abscisic acid levels, as further verified by transcriptomic analyses of their synthetic genes. Overexpression of an auxin synthetic gene GmYUC2a also affected SL and KAR signaling genes. GmMAX2a physically interacted with SL/KAR receptors GmD14s, GmKAIs, and GmD14Ls with different binding affinities, depending on variations in the critical amino acids, forming active D14/KAI‐SCFMAX2 complexes. The knockdown mutant roots of the nodule‐specifically expressing GmKAIs and GmD14Ls gave fewer nodules, with altered expression of several early nodulation genes. The expression levels of GmKAIs, and GmD14Ls were markedly changed in GmMAX2a mutant roots, so did their target repressor genes GmD53s and GmSMAX1s. Thus, SL and KAR signaling were involved in soybean–rhizobia interaction and nodulation partly through interactions with hormones, and this may explain the different effects of MXA2 orthologs on legume determinate and indeterminate nodulation. The study provides fresh insights into the roles of GmMAX2‐mediated SL/KAR signaling in soybean root hair and nodule formation. Significance Statement: Soybean strigolactone and karrikin signaling genes are specifically expressed in root and nodules and respond to rhizobia infection. GmMAX2a mutant roots display altered root hairs, nodule numbers, and hormone levels, and GmMAX2a interacts with GmD14s, GmKAIs, and GmD14Ls, the last two of which gave fewer nodules in their knockdown mutants. The study expands the functions of GmMAX2‐mediated SL/KAR signaling in modulating root hair and nodule formation, and interactions with auxins and other hormone signaling. [ABSTRACT FROM AUTHOR]

The article discusses a study which examined the properties of large earthquakes that have occurred along the Himalayan orogenic belt, particularly the 2005 Kashmir earthquake in the Northwestern Himalaya Syntaxis. Topics covered include the major tectonic feature for source area of the 2005 Kashmir earthquake, the relocations of the earthquake and its aftershocks, and the source parameters and rupture process of the earthquake.

The lithosphere-asthenosphere boundary (LAB) is the seismic discontinuity with negative velocity contrasts in the upper mantle. Seismic detections on the LAB are of great significance in understanding the plate tectonics, mantle convection and lithospheric evolution. In this paper, we study the LAB in the Izu-Bonin subduction zone using four deep earthquakes recorded by the permanent and temporary seismic networks of the USArray. The LAB is clearly revealed with sP precursors (sdP) through the linear slant stacking. As illustrated by reflected points of the identified sdP phases, the depth of LAB beneath the Izu-Bonin Arc (IBA) is about 65 km with a range of 60-68 km. The identified sdP phases with opposite polarities relative to sP phases have the average relative amplitude of 0.21, which means a 3.7% velocity drop and implies partial melting in the asthenosphere. On the basis of the crustal age data, the lithosphere beneath the IBA is located at the ~ 1100 °C isotherm calculated with the GDH1 model. Compared to tectonically stable areas, such as the West Philippine Basin (WPB) and Parece Vela Basin (PVB) in the Philippine Sea, the lithosphere beneath the Izu-Bonin area shows the obvious lithospheric thinning. According to the geodynamic and petrological studies, the oceanic lithospheric thinning phenomenon can be attributed to the strong erosion of the small-scale convection in the mantle wedge enriched in volatiles and melts. [ABSTRACT FROM AUTHOR]

Hybrid-polarimetric SAR (synthetic aperture radar) is a new SAR mode, with relatively simple architecture, low cost, and wide swath, which will be carried by several Earth-observing systems from now to the near future. Here, we show how the second Stokes parameter of hybrid-polarimetric SAR can be employed to detect oil on the ocean surface using the classic well-known Otsu threshold methodology, in relation to contributions from different polarizations and dampening effects on backscatter intensity, neglecting the specific scattering mechanisms and oil types for an oil-covered surface. The detection methodology is demonstrated to be reliable in three example cases: oil-on-water experiments conducted by the Norwegian Clean Seas Association, natural oil seeps from the Gulf of Mexico, and observations from the Deep Water Horizon oil spill disaster in 2010. [ABSTRACT FROM AUTHOR]

The undulation and characteristics of the Lehmann discontinuity at the base of the Low Velocity Zone in the upper mantle are significant for understanding the coupling between the lithosphere and asthenosphere, and corresponding geodynamic processes. Vertical waveform data from six earthquakes with focal depths between 75 and 150 km and magnitudes M 5.0-6.0 since 2004 were collected from the short-period Hi-net array. Selected waveform data were processed for each event network pair using the Nth-root slant stack method to retrieve the SdP conversion phases from the possible 220 km (Lehmann) discontinuity. The conversion points related to the SdP phases show that there is a clear and flat velocity interface around 230 km, suggesting that there is a sinking of the Lehmann discontinuity beneath Tonga with no obvious undulation. The 230 km depth of the Lehmann discontinuity in this location could be explained by an hypothesis of transition in the deformation mechanism from dislocation creep to diffusion creep. [ABSTRACT FROM AUTHOR]

The SdP, pdP and sdP phases are picked up with the Nth root slant stack method from the digital waveform data recorded by the networks and arrays in USA, Germany and Switzerland for the earthquakes occurring beneath Izu-Bonin and Japan Sea. The mantle discontinuities and the effects of subducting slab on the 660 km and 410 km discontinuities are studied. It is found that there are mantle discontinuities existing at the depths of 170, 220, 300, 410, 660, 850 and 1150 km. Beneath Izu-Bonin, the 410 km discontinuity is elevated, while the 660 km discontinuity is depressed; for both discontinuities, there are regionalized differences. Beneath Japan Sea, however, there is no depth variation of the 410 km discontinuity, and the 660 km discontinuity is depressed without obvious effect of the subducting slab. [ABSTRACT FROM AUTHOR]

Shows evidences for reflective and refractive phases associated with the 410 kilometer and 660 kilometer discontinuities. Topographies of seismic velocity discontinuities; Penetrations of subducting slabs beneath the Sea of Okhotsk; Use of the Nth root slant stack and digital records from networks in Germany and western United States.