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Mineralogy, geochronology, and geochemistry of the calc-alkaline Um Takha white granite pluton, South Sinai, Egypt
No full textThe Um Takha white granite pluton (UTP) is exposed in west central Sinai (Egypt), in the northernmost segment of the Neoproterozoic Arabian-Nubian Shield (ANS). It is a member of the youngest suite of calc-alkaline granites in south Sinai. The UTP intrudes metamorphosed country rocks and diorites and is in turn intruded by the Serbal alkaline granite pluton. The UTP comprises a single phase of leucocratic monzogranite that contains alkali feldspar, plagioclase, quartz, biotite, and rare muscovite. U-Pb ion probe zircon dating for two samples of the white granite yields ages of 614.9 ± 6.3 and 581.5 ± 10.9 Ma, but the younger sample reveals abundant evidence that its zircons were affected by late corrosive fluids (e.g., discordance and patchy cathodoluminescence zoning); the 614.9 ± 6.3 Ma age is preferred. Geochemically, the UTP displays a limited compositional range (SiO₂ = 72.9–75.1 wt%) of mostly high-K calc-alkaline rocks of metaluminous to weakly peraluminous character, typical of the calc-alkaline granitoids of the early post-collisional stage of the northern ANS. The variation diagrams and parallel rare-earth element (REE) patterns for the white granite samples (n = 22) suggest that they represent one cogenetic suite. The UTP was likely generated by partial melting of a Na-rich amphibole-bearing tonalite source from the juvenile crust. This is consistent with the Hf isotope ratios of zircons from the UTP, which consistently yield positive εHf(t) values. The proposed trigger for the formation of the UTP is lithospheric delamination; its emplacement was associated with extensive denudation of the pre-630 Ma orogenic edifice as well as the 630–600 Ma post-collisional products, heat transfer into the lower crust, and post-collisional magmatism. Although the UTP is a cogenetic body, the traditional liquid-line-of-descent fractional crystallization approach fails to explain the large dynamic range of trace element contents over a limited range in major elements. We show that an alternative variable-proportion cumulate-liquid sampling interpretation of the whole-rock compositions, in which the most evolved sample represents a liquid composition and the least evolved sample is a low melt-fraction crystal mush, offers a physically reasonable scenario for the observed suite
Tipping point in North American Arctic-Boreal carbon sink persists in new generation Earth system models despite reduced uncertainty
No full textEstimating the impacts of climate change on the global carbon cycle relies on projections from Earth system models (ESMs). While ESMs currently project large warming in the high northern latitudes, the magnitude and sign of the future carbon balance of Arctic-Boreal ecosystems are highly uncertain. The new generation of increased complexity ESMs in the Intergovernmental Panel on Climate Change Sixth Assessment Report (IPCC AR6) is intended to improve future climate projections. Here, we benchmark the Coupled Model Intercomparison Project (CMIP) 5 and 6 (8 CMIP5 members and 12 CMIP6 members) with the International Land Model Benchmarking (ILAMB) tool over the region of NASA's Arctic-Boreal vulnerability experiment (ABoVE) in North America. We show that the projected average net biome production (NBP) in 2100 from CMIP6 is higher than that from CMIP5 in the ABoVE domain, despite the model spread being slightly narrower. Overall, CMIP6 shows better agreement with contemporary observed carbon cycle variables (photosynthesis, respiration, biomass) than CMIP5, except for soil carbon and turnover time. Although both CMIP ensemble members project the ABoVE domain will remain a carbon sink by the end of the 21st century, the sink strength in CMIP6 increases with CO₂ emissions. CMIP5 and CMIP6 ensembles indicate a tipping point defined here as a negative inflection point in the NBP curve by 2050–2080 independently of the shared socioeconomic pathway (SSP) for CMIP6 or representative concentration pathway (RCP) for CMIP5. The model ensembles therefore suggest that, if the carbon sink strength keeps declining throughout the 21st century, the Arctic-Boreal ecosystems in North America may become a carbon source over the next century
A Text-guided Protein Design Framework
No full textCurrent AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level properties. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP that aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that generates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We empirically verify the effectiveness of ProteinDT from three aspects: (1) consistently superior performance on four out of six protein property prediction benchmarks; (2) over 90% accuracy for text-guided protein generation; and (3) promising results for zero-shot text-guided protein editing
Multiview Compressive Coding for 3D Reconstruction
No full textA central goal of visual recognition is to understand objects and scenes from a single image. 2D recognition has witnessed tremendous progress thanks to large-scale learning and general-purpose representations. Comparatively, 3D poses new challenges stemming from occlusions not depicted in the image. Prior works try to overcome these by inferring from multiple views or rely on scarce CAD models and category-specific priors which hinder scaling to novel settings. In this work, we explore single-view 3D reconstruction by learning generalizable representations inspired by advances in self-supervised learning. We introduce a simple framework that operates on 3D points of single objects or whole scenes coupled with category-agnostic large-scale training from diverse RGB-D videos. Our model, Multiview Compressive Coding (MCC), learns to compress the input appearance and geometry to predict the 3D structure by querying a 3D-aware decoder. MCC's generality and efficiency allow it to learn from large-scale and diverse data sources with strong generalization to novel objects imagined by DALL⋅E 2 or captured in-the-wild with an iPhone
Bacterial Form I’ rubisco has smaller carbon isotope fractionation than its Form I counterpart
No full textForm I rubiscos evolved in Cyanobacteria ≥2.5 billion years ago and are enzymatically unique due to the presence of small subunits (RbcS) that cap both ends of an octameric large subunit (RbcL) rubisco assembly to form a hexadecameric (L₈S₈) holoenzyme. Although RbcS was previously thought to be integral to Form I rubisco stability, the recent discovery of a closely related sister clade of octameric rubiscos (Form I’; L₈) demonstrates that the enzyme complex assembles without small subunits (Banda et al. 2020). Rubisco also displays a kinetic isotope effect (KIE) where the 3PG product is depleted in ¹³C relative to ¹²C. In Cyanobacteria only two Form I KIE measurements exist, making interpretation of bacterial carbon isotope data difficult. To aid comparison, we measured in vitro the KIEs of Form I’ (Candidatus Promineofilum breve) and Form I (Synechococcus elongatus PCC 6301) rubiscos and found the KIE to be smaller in the L₈ rubisco (16.25 ± 1.36‰ vs. 22.42 ± 2.37‰ respectively). Therefore, while small subunits may not be necessary for protein stability, they may affect the KIE. Our findings may provide insight into the function of RbcS and allow more refined interpretation of environmental carbon isotope data
Systematic comparison of risky choices in humans and monkeys
No full textThe past decades have seen tremendous progress in fundamental studies on economic choice in humans. However, elucidation of the underlying neuronal processes requires invasive neurophysiological studies that are met with difficulties in humans. Monkeys as evolutionary closest relatives offer a solution. The animals display sophisticated and well-controllable behavior that allows to implement key constructs of proven economic choice theories. However, the similarity of economic choice between the two species has never been systematically investigated. We investigated compliance with the independence axiom (IA) of expected utility theory as one of the most demanding choice tests and compared IA violations between humans and monkeys. Using generalized linear modeling and cumulative prospect theory (CPT), we found that humans and monkeys made comparable risky choices, although their subjective values (utilities) differed. These results suggest similar fundamental choice mechanism across these primate species and encourage to study their underlying neurophysiological mechanisms
Mob4 is essential for spermatogenesis in Drosophila melanogaster
No full textGamete formation is essential for sexual reproduction in metazoans. In males, spermatogenesis gives rise to interconnected spermatids that have to differentiate and individualize into mature sperm. InDrosophila melanogaster, individualization of spermatids requires the formation of individualization complexes that synchronously move along the sperm bundles. Here, we show that Mob4, a member of the Mps-one binder family, is essential for male fertility but has no detectable role on female fertility. We describe the function of Mob4 during spermatid individualization, showing that Mob4 is required for proper axonemal structure and that the loss of Mob4 leads to male sterility associated with defective spermatid individualization and absence of mature sperm in the seminal vesicles. Transmission electron micrographs of Mob4ᴿᴺᴬᶦ developing spermatids revealed defects in axoneme structure and abnormal mitochondria biogenesis. Importantly, we find that male fertility is impaired upon depletion of other STRIPAK components, suggesting that Mob4 acts through STRIPAK to support spermiogenesis. As we show that expression of the human Mob4 gene effectively rescues all phenotypes of Mob4 downregulation, the gene is not only evolutionary but also functionally conserved. We propose that Mob4 plays a role in regulating the microtubule- and actin-cytoskeleton during spermatogenesis. This study advances our understanding of male infertility by uncovering Mob4 as a novel gene required for sperm individualization
Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations
No full textHIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120/gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops, and in fully-saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops. To investigate changes resulting from sub-stoichiometric CD4 binding, we solved 3.4Å and 3.9Å single-particle cryo-EM structures of soluble, native-like Envs bound to one or two CD4 molecules. Env trimer bound to one CD4 adopted the closed, prefusion Env state. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state that included gp120 outward rotation but maintained the prefusion, three-stranded gp120 bridging sheet and showed only partial V1V2 displacement and V3 exposure. We conclude that engagement of one CD4 molecule was insufficient to stimulate CD4-induced conformational changes, while binding two CD4 molecules led to Env opening in CD4-bound protomers only. Together, these results illuminate HIV-1 Env intermediate conformations and illustrate the structural plasticity of HIV-1 Env
Dysregulated mammalian estrus cycle rescued by timed activation of VIP neurons in the circadian pacemaker and late afternoon light exposure
No full textJet lag and shift work disrupt the menstrual cycle and decrease fertility. The circadian pacemaker, the suprachiasmatic nucleus (SCN), is known to modulate ovulation, but the mechanism is unclear. Here we explore this connection by tracking the dynamics of vasoactive intestinal peptide (VIP)-expressing neurons in the SCN in freely-behaving mice. We show that SCNVIPactivity is time-of-day- and sex-dependent, and estrous-state-dependent in late afternoon, gating downstream activation of GnRH neurons. Afternoon light, as well as specific activation of SCNVIPneurons, rescues estrous cycle regularity and egg release in animals in altered light conditions, emphasizing the role of SCNVIPneurons as a time-dependent light-responsive switch. Our results reveal the dynamic mechanism by which SCNVIPneurons mediate light responses to regulate estrous states and demonstrate light-induced fertility rescue.One Sentence SummaryModulating and recording the activity of suprachiasmatic VIP neurons in freely behaving mice reveals their regulation of fertility by mediating the response to late afternoon light