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We explore the response of ground motions to topography during large crustal fault earthquakes by simulating several magnitude 6.5–7.0 rupture scenarios on the Seattle fault, Washington State. Kinematic simulations are run using a 3D spectral element code and a detailed seismic velocity model for the Puget Sound region. This model includes realistic surface topography and a near-surface low-velocity layer; a mesh spacing of ∼30 m at the surface allows modeling of ground motions up to 3 Hz. We simulate 20 earthquake scenarios using different slip distributions and hypocenter locations on a planar fault surface. Results indicate that average ground motions in simulations with and without topography are similar. However, shaking amplification is common at topographic highs, and more than a quarter of all sites experience short-period (≤2 s) ground-motion amplification greater than 25%–35%, compared with models without topography. Comparisons of peak ground velocity at the top and bottom of topographic features demonstrate that amplification is sensitive to period, with the greatest amplifications typically manifesting near a topographic feature’s estimated resonance frequency and along azimuths perpendicular to its primary axis of elongation. However, interevent variability in topographic response can be significant, particularly at shorter periods (

The 2021 US National Seismic Hazard Model (NSHM) for the State of Hawaii updates the previous two-decade-old assessment by incorporating new data and modeling techniques to improve the underlying ground shaking forecasts of tectonic-fault, tectonic-flexure, volcanic, and caldera collapse earthquakes. Two earthquake ground shaking hazard forecasts (public policy and research) are produced that differ in how they account for declustered catalogs. The earthquake source model is based on (1) declustered earthquake catalogs smoothed with adaptive methods, (2) earthquake rate forecasts based on three temporally varying 60-year time periods, (3) maximum magnitude criteria that extend to larger earthquakes than previously considered, (4) a separate Kīlauea-specific seismogenic caldera collapse model that accounts for clustered event behavior observed during the 2018 eruption, and (5) fault ruptures that consider historical seismicity, GPS-based strain rates, and a new Quaternary fault database. Two new Hawaii-specific ground motion models (GMMs) and five additional global models consistent with Hawaii shaking data are used to forecast ground shaking at 23 spectral periods and peak parameters. Site effects are calculated using western US and Hawaii specific empirical equations and provide shaking forecasts for 8 site classes. For most sites the new analysis results in similar spectral accelerations as those in the 2001 NSHM, with a few exceptions caused mostly by GMM changes. Ground motions are the highest in the southern portion of the Island of Hawai’i due to high rates of forecasted earthquakes on décollement faults. Shaking decays to the northwest where lower earthquake rates result from flexure of the tectonic plate. Large epistemic uncertainties in source characterizations and GMMs lead to an overall high uncertainty (more than a factor of 3) in ground shaking at Honolulu and Hilo. The new shaking model indicates significant chances of slight or greater damaging ground motions across most of the island chain.

Background Life expectancies for patients with congenital heart disease (CHD) have dramatically increased in recent years, accompanied by a rise in atrial fibrillation (AF) prevalence. Data on AF ablation strategy and outcomes are limited in CHD. Purpose We aimed to investigate the characteristics of CHD patients presenting for AF ablation and their outcomes. Methods A multicenter, retrospective analysis was performed of CHD patients undergoing AF ablation between 2004 and 2020 at 13 participating centers. The severity of CHD was classified using the 2014 PACES/HRS guidelines. Clinical data were collected including ablation strategy and follow up. One-year procedural success was defined as freedom from AF in the absence of antiarrhythmic drugs (AADs, complete) or including previously failed AADs (partial). Results Of 240 patients, 127 (53.4%) had persistent AF, 62.5% were male, and mean age was 55.2±0.9 years. CHD complexity categories included 147 (61.3%) simple, 69 (28.8%) intermediate and 25 (10.4%) severe. The most common CHD type was atrial septal defect (n=78). More complex CHD conditions included transposition of the great arteries (n=14), anomalous pulmonary veins (n=13), tetralogy of Fallot (n=8), cor triatriatum (n=7), single ventricle physiology (n=2), among others. The majority (71.3%) of patients had AF despite at least one AAD. 46 patients (22.1%) had a reduced systemic ventricular ejection fraction Conclusion AF ablation in this complex population was safe and resulted in AF control in the majority of patients. Future work should address the most appropriate ablation targets in the challenging population. Funding Acknowledgement Type of funding sources: None.

The prevalence of obesity and its comorbidities has sparked a worldwide concern to address rates of adipose tissue accrual. Recent studies have demonstrated a novel role of Zyflamend, a blend of natural herbal extracts, in regulating lipid metabolism in several cancer cell lines through the activation of the AMPK signalling pathway. Yet, the role of Zyflamend in adipogenic differentiation and lipid metabolism remains largely unexplored. The objective of this study is to investigate the effects of Zyflamend on white 3T3-MBX pre-adipocyte differentiation and elucidate the molecular mechanisms. We demonstrate that Zyflamend treatment altered cell cycle progression, attenuated proliferation, and increased cell death of 3T3-MBX pre-adipocytes. In addition, treatment with Zyflamend inhibited lipid accumulation during the differentiation of 3T3-MBX cells, consistent with decreased expression of lipogenic genes and increased lipolysis. Mechanistically, Zyflamend-induced alterations in adipogenesis were mediated, at least in part, through the activation of AMPK, PKA, and JNK. Inhibition of AMPK partially reversed Zyflamend-induced inhibition of differentiation, whereas the inhibition of either JNK or PKA fully restored adipocyte differentiation and decreased lipolysis. Taken together, the present study demonstrates that Zyflamend, as a novel anti-adipogenic bioactive mix, inhibits adipocyte differentiation through the activation of the PKA and JNK pathways. Abbreviation 7-AAD: 7-amino-actinomycin D; ACC: acetyl-CoA carboxylase; AKT: protein kinase B; AMPK: AMP-activated protein kinase; ATGL: adipose triglyceride lipase; C/EBPα: CCAAT-enhancer binding protein alpha; DMEM: Dulbecco’s Modified Eagle Medium; DMSO: dimethyl sulphoxide; DTT: dithiothreitol; EGTA: ethylene glycol-bis-(2-aminoethyl)-N,N,N’,N’-tetraacetic acid; ERK: extracellular signal–regulated kinases; FASN: fatty acid synthase; FBS: foetal bovine serum; GLUT: glucose transporter; HSL: hormone-sensitive lipase; IR: insulin receptor; IRS: insulin receptor substrate; JNK: c-JUN N-terminal kinase; MGL: monoacylglycerol lipase; NaF: sodium fluoride; NF-κB: nuclear factor kappa-light-chain-enhancer of activated B cells; PBS: phosphate buffered- saline; PCB: pyruvate carboxylase; PDE: phosphodiesterase; PKA: protein kinase cAMP-dependent; PMSF: phenylmethylsulfonyl fluoride; PPARγ: perilipin peroxisome proliferator-activated receptor gamma; PREF-1: pre-adipocyte factor 1; PVDF: polyvinylidene fluoride; RIPA: radio-immunoprecipitation assay; SDS-PAGE: sodium dodecyl sulphate polyacrylamide gel electrophoresis; SEM: standard error of the mean; SOX9: suppressor of cytokine signalling 9; TGs: triacylglycerols.

Viruses must effectively remodel host cellular pathways to replicate and evade immune defenses, and they must do so with limited genomic coding capacity. Targeting post-translational modification (PTM) pathways provides a mechanism by which viruses can broadly and rapidly transform a hostile host environment into a hospitable one. We use mass spectrometry-based proteomics to quantify changes in protein abundance and two PTM types-phosphorylation and ubiquitination-in response to HIV-1 infection with viruses harboring targeted deletions of a subset of HIV-1 genes. PTM analysis reveals a requirement for Aurora kinase activity in HIV-1 infection and identified putative substrates of a phosphatase that is degraded during infection. Finally, we demonstrate that the HIV-1 Vpr protein inhibits histone H1 ubiquitination, leading to defects in DNA repair., Cell Reports, 39 (2), ISSN:2666-3864, ISSN:2211-1247

SummaryOverlapping coding regions balance selective forces between multiple genes. One possible division of nucleotide sequence is that the predominant selective force on a particular nucleotide can be attributed to just one gene. While this arrangement has been observed in regions in which one gene is structured and the other is disordered, we sought to explore how overlapping genes balance constraints when both protein products are structured over the same sequence. We use a combination of sequence analysis, functional assays and selection experiments to examine an overlapped region in HIV-1 that encodes helical regions in both Env and Rev. We find that functional segregation occurs even in this overlap, with each protein spacing its functional residues in a manner that allows a mutable non-binding face of one helix to encode important functional residues on a charged face in the other helix. Additionally, our experiments reveal novel and critical functional residues in Env and have implications for the therapeutic targeting of HIV-1.

Background Invasive lobular carcinoma (ILC) is associated with high re-excision rates following breast-conserving surgery (BCS). The correlation between lesion size on different imaging modalities and final tumor size has not been well characterized. Methods A prospective database of patients with stage I-III breast cancer undergoing BCS between 2006 and 2016 was reviewed. Pearson correlation analysis was used to correlate tumor size on breast imaging to final pathology. Results Of these, 111 patients with ILC were identified. Mean lesion size was 1.93 cm for MMG, 1.61 cm for US, and 2.51 cm for MRI. Mean tumor size on surgical excision was 2.64 cm. The correlation coefficient between pathology and the different imaging modalities were as follows: MMG .17, US 0.37, and MRI .58. Actual tumor size was underestimated by 1 cm in 27.1% of MMGs, 50% of USs, and in 13.3% of MRIs. 38 patients (34.2%) underwent re-excision. No differences in re-excision rates were noted in patients with and without MRI, 30.3% vs 40.0%, respectively (P = .31). Conclusion While MRI provides a better estimate of tumor size than MMG and US, the size of the tumor on imaging only weakly correlated with pathology. The use of MRI does not decrease re-excision rates.

A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein–protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19. A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.

We have developed a platform for quantitative genetic interaction mapping using viral infectivity as a functional readout and constructed a viral host-dependency epistasis map (vE-MAP) of 356 human genes linked to HIV function, comprising >63,000 pairwise genetic perturbations. The vE-MAP provides an expansive view of the genetic dependencies underlying HIV infection and can be used to identify drug targets and study viral mutations. We found that the RNA deadenylase complex, CNOT, is a central player in the vE-MAP and show that knockout of CNOT1, 10, and 11 suppressed HIV infection in primary Tcells by upregulating innate immunity pathways. This phenotype was rescued by deletion of IRF7, a transcription factor regulating interferon-stimulated genes, revealing a previously unrecognized host signaling pathway involved in HIV infection. The vE-MAP represents a generic platform that can be used to study the global effects of howdifferent pathogens hijack and rewire the host during infection.

SUMMARYViruses must effectively remodel host cellular pathways to replicate and evade immune defenses, and they must do so with limited genomic coding capacity. Targeting post-translational modification (PTM) pathways provides a mechanism by which viruses can broadly and rapidly transform a hostile host environment into a hospitable one. We used quantitative proteomics to measure changes in two PTM types – phosphorylation and ubiquitination – in response to HIV-1 infection with viruses harboring targeted deletions of a subset of HIV-1 genes. PTM analysis revealed a requirement for Aurora kinase A activity in HIV-1 infection and furthermore revealed that AMP-activated kinase activity is modulated during infection via HIV-1 Vif-mediated degradation of B56-containing protein phosphatase 2A (PP2A). Finally, we demonstrated that the Cullin4A-DDB1-DCAF1 E3 ubiquitin ligase ubiquitinates histone H1 somatic isoforms and that HIV-1 Vpr inhibits this process, leading to defects in DNA repair. Thus, global PTM profiling of infected cells serves as an effective tool for uncovering specific mechanisms of host pathway modulation.

We synthesized and screened a unique 46 656-member library composed of unnatural amino acids that revealed several hits against RRE IIB RNA. Among the hit peptides identified, peptide 4A5 was found to be selective against competitor RNAs and inhibited HIV-1 Rev-RRE RNA interaction in cell culture in a p24 ELISA assay. Biophysical characterization in a ribonuclease protection assay suggested that 4A5 bound to the stem-loop region in RRE IIB while SHAPE MaP probing with 234 nt RRE RNA indicated additional interaction with secondary Rev binding sites. Taken together, our investigation suggests that HIV replication is inhibited by 4A5 blocking binding of Rev and subsequent multimerization.

Viruses are completely dependent upon cellular machinery to support replication and have therefore developed strategies to co-opt cellular processes to optimize infection and counter host immune defenses. Many viruses, including human immunodeficiency virus type 1 (HIV-1), encode a relatively small number of genes. Viruses with limited genetic content often encode multifunctional proteins that function at multiple stages of the viral replication cycle. In this review, we discuss the functions of HIV-1 regulatory (Tat and Rev) and accessory (Vif, Vpr, Vpu, and Nef) proteins. Each of these proteins has a highly conserved primary activity; however, numerous additional activities have been attributed to these viral proteins. We explore the possibility that HIV-1 proteins leverage their multifunctional nature to alter host transcriptional networks to elicit a diverse set of cellular responses. Although these transcriptional effects appear to benefit the virus, it is not yet clear whether they are strongly selected for during viral evolution or are a ripple effect from the primary function. As our detailed knowledge of these viral proteins improves, we will undoubtedly uncover how the multifunctional nature of these HIV-1 regulatory and accessory proteins, and in particular their transcriptional functions, work to drive viral pathogenesis.

When the axial gain length of a stimulated Raman microscope is less than about 40% of the emission wavelength significant dipole-like ballistic backscatter will occur. Here we analyze a scanning microscope configured with orthogonal water dipping pump and probe objectives that satisfies this criterion. The pump beam focus may be a Gaussian spot or a droplet Bessel beam which minimizes the secondary Bessel beam lobes and provides multiple simultaneous pump focal spot regions. Radial and linearly polarized pump beams enable backscattered polarized signals along both transverse axes of the probe beam. Low level Mie backscatter is the primary photon noise source which should enable rapid sub-wavelength resolution 3-dimensional imaging of label-free Raman contrast for in-vivo pathology, as well as, imaging physiologic concentrations of Raman labelled metabolites and drugs.

Pyruvate kinase M2 is a critical enzyme that regulates cell metabolism and growth under different physiological conditions. In its metabolic role, pyruvate kinase M2 catalyzes the last glycolytic step which converts phosphoenolpyruvate to pyruvate with the generation of ATP. Beyond this metabolic role in glycolysis, PKM2 regulates gene expression in the nucleus, phosphorylates several essential proteins that regulate major cell signaling pathways, and contribute to the redox homeostasis of cancer cells. The expression of PKM2 has been demonstrated to be significantly elevated in several types of cancer, and the overall inflammatory response. The unusual pattern of PKM2 expression inspired scientists to investigate the unrevealed functions of PKM2 and the therapeutic potential of targeting PKM2 in cancer and other disorders. Therefore, the purpose of this review is to discuss the mechanistic and therapeutic potential of targeting PKM2 with the focus on cancer metabolism, redox homeostasis, inflammation, and metabolic disorders. This review highlights and provides insight into the metabolic and non-metabolic functions of PKM2 and its relevant association with health and disease.

Summary The Cullin-RING E3 ligase (CRL) family is commonly hijacked by pathogens to redirect the host ubiquitin proteasome machinery to specific targets. During HIV infection, CRL5 is hijacked by HIV Vif to target viral restriction factors of the APOBEC3 family for ubiquitination and degradation. Here, using a quantitative proteomics approach, we identify the E3 ligase ARIH2 as a regulator of CRL5-mediated APOBEC3 degradation. The CUL5Vif/CBFs complex recruits ARIH2 where it acts to transfer ubiquitin directly to the APOBEC3 targets. ARIH2 is essential for CRL5-dependent HIV infectivity in primary CD4+ T cells. Furthermore, we show that ARIH2 cooperates with CRL5 to prime other cellular substrates for polyubiquitination, suggesting this may represent a general mechanism beyond HIV infection and APOBEC3 degradation. Taken together, these data identify ARIH2 as a co-factor in the Vif-hijacked CRL5 complex that contributes to HIV infectivity and demonstrate the operation of the E1-E2-E3/E3-substrate ubiquitination mechanism in a viral infection context.

The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription. It is not clear how the N protein mediates such distinct functions. The N protein contains two RNA-binding domains surrounded by regions of intrinsic disorder. Phosphorylation of the central disordered region promotes the protein's transcriptional function, but the underlying mechanism is not known. Here, we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates. Unmodified N protein forms partially ordered gel-like condensates and discrete 15-nm particles based on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces these interactions, generating a more liquid-like droplet. We propose that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing.

Following overland and maritime trade routes, early Muslims reached China within a century after the Prophet Muhammad (570–632) lived, when the Chinese and Islamic empires were the superpowers of their day, engaging each other in instances of both competition and collaboration: military, economic and diplomatic. Exchanges between China and the Islamic world have produced significant technological and cultural developments, and set the stage for ongoing relations between the two civilizations that helped shape world history and continue to influence global affairs today. The arrival of Islam more than 1200 years ago also resulted in a sizeable Muslim minority population in China, who play an important role between the two civilizations: sometimes as cultural intermediaries, sometimes as political pawns. The following is an overview of the history of Chinese–Islamic relations, including historical and contemporary involvement by China’s internal Muslim populations, with a survey of connections betwe...

Viruses are obligate parasites that rely heavily on host cellular processes for replication. The small number of proteins typically encoded by a virus is faced with selection pressures that lead to the evolution of distinctive structural properties, allowing each protein to maintain its function under constraints such as small genome size, high mutation rate, and rapidly changing fitness conditions. One common strategy for this evolution is to utilize small building blocks to generate protein oligomers that assemble in multiple ways, thereby diversifying protein function and regulation. In this review, we discuss specific cases that illustrate how oligomerization is used to generate a single defined functional state, to modulate activity via different oligomeric states, or to generate multiple functional forms via different oligomeric states.

HIV replication requires the nuclear export of essential, intron-containing viral RNAs. To facilitate export, HIV encodes the viral accessory protein Rev which binds unspliced and partially spliced viral RNAs and creates a ribonucleoprotein complex that recruits the cellular Chromosome maintenance factor 1 export machinery. Exporting RNAs in this manner bypasses the necessity for complete splicing as a prerequisite for mRNA export, and allows intron-containing RNAs to reach the cytoplasm intact for translation and virus packaging. Recent structural studies have revealed that this entire complex exhibits remarkable plasticity at many levels of organization, including RNA folding, protein-RNA recognition, multimer formation, and host factor recruitment. In this review, we explore each aspect of plasticity from structural, functional, and possible therapeutic viewpoints. WIREs RNA 2016, 7:470-486. doi: 10.1002/wrna.1342 For further resources related to this article, please visit the WIREs website.

OBJECTIVES: The prevalence of obesity and its comorbidities has sparked a worldwide concern to address rates of adipose tissue accrual. Recent studies have demonstrated a novel role of Zyflamend, a natural herbal extract, in regulating lipid metabolism in several cancer cell lines through the activation of the AMPK signaling pathway. Yet, the role of Zyflamend in adipogenic differentiation and lipid metabolism remains largely unexplored. The objective of this study is to investigate the effects of Zyflamend on white 3T3-MBX pre-adipocyte differentiation and elucidate the molecular mechanisms. METHODS: 3T3-MBX pre-adipocytes were treated with Zyflamend, and the expression of various key adipogenic and lipolytic regulators was examined. We also investigated the effects of Zyflamend on pre-adipocyte survival, proliferation, and cell cycle. RESULTS: Zyflamend treatment altered cell cycle progression, attenuated proliferation, and increased cell death of 3T3-MBX pre-adipocytes. In addition, treatment with Zyflamend inhibited lipid accumulation during the differentiation of 3T3-MBX cells, consistent with decreased expression of lipogenic genes and increased lipolysis. Mechanistically, Zyflamend-induced alterations in adipogenesis were mediated, at least in part, through the activation of AMPK, PKA, and JNK. Inhibition of AMPK partially reversed Zyflamend-induced inhibition of differentiation, whereas the inhibition of either JNK or PKA fully restored adipocyte differentiation and decreased lipolysis. CONCLUSIONS: Taken together, the present study demonstrates that Zyflamend, as a novel anti-adipogenic bioactive mix, inhibits adipocyte differentiation through the activation of PKA and JNK pathways.Our findings suggest that Zyflamend supplementation might help in developing novel anti-obesity therapeutic strategies. FUNDING SOURCES: This work was supported by the National Institute of Diabetes and Digestive and Kidney Diseases (R00DK100736) to A.B.