Brazilian Atlantic rainforest under attack | Science

Brazil has committed to ambitious goals, including the reforestation of 12 million hectares (1). However, a recent proposal by Brazil’s Congress (2, 3) puts at risk the Atlantic Forest, one of the world’s most threatened biomes (4). The Provisional Measure (MP) 1150/2022 aims to change the Atlantic Forest Law (11.428/2006) and the Forest Code (12.651/2012) by loosening restrictions on removing native vegetation. After Brazil’s Chamber of Deputies and Senate approved the proposal in May, President Lula rejected it, but the Congress could overturn the presidential veto. National and international pressure are essential to persuade Brazil’s Congress to comply with the presidential veto and prevent further attacks to the Atlantic Forest.

Bills undermine Brazil’s environmental goals | Science

After 4 years of regression in Brazil’s environmental policies, the administration of President Luiz Inácio Lula da Silva has been trying to resume an environmental agenda (1). However, the Brazilian Chamber of Deputies—led by Arthur Lira, a supporter of former President Jair Bolsonaro (2)—has recently approved a provisional measure (MP) and a bill, MP1154/2023 and PL490, that would hinder Brazil’s ability to control deforestation and threats to Indigenous lands. If these bills are approved by the Senate and signed into law by the president, global trade partners should reconsider their import agreements with Brazil.

Silent summers: The decline of cicadas | Science

HomeScienceVol. 381, No. 6657Silent summers: The decline of cicadasBack To Vol. 381, No. 6657 Full accessLetter Share on Silent summers: The decline of cicadasHong Yang [email protected], Xiaohua Xiang, [...] , Xiaoling Wu, Julian R. Thompson, and Roger J. Flower+2 authors fewerAuthors Info & AffiliationsScience3 Aug 2023Vol 381, Issue 6657p. 490DOI: 10.1126/science.adj0783 PREVIOUS ARTICLEDavid …

Turning the tide on obesity? | Science

Genetics, ultraprocessed foods, portion distortion, sweetened beverages, screen time, food addiction, intestinal microbiota, diet culture, weight stigma, food insecurity—all have been implicated in the “obesity epidemic.” More than a billion people ...

Widespread reforestation before European influence on Amazonia

An estimated 90 to 95% of Indigenous people in Amazonia died after European contact. This population collapse is postulated to have caused decreases in atmospheric carbon dioxide concentrations at around 1610 CE, as a result of a wave of land abandonment in the wake of disease, slavery, and warfare, whereby the attendant reversion to forest substantially increased terrestrial carbon sequestration. On the basis of 39 Amazonian fossil pollen records, we show that there was no synchronous reforestation event associated with such an atmospheric carbon dioxide response after European arrival in Amazonia. Instead, we find that, at most sites, land abandonment and forest regrowth began about 300 to 600 years before European arrival. Pre-European pandemics, social strife, or environmental change may have contributed to these early site abandonments and ecological shifts.

The human dimension of biodiversity changes on islands

Islands are among the last regions on Earth settled and transformed by human activities, and they provide replicated model systems for analysis of how people affect ecological functions. By analyzing 27 representative fossil pollen sequences encompassing the past 5000 years from islands globally, we quantified the rates of vegetation compositional change before and after human arrival. After human arrival, rates of turnover accelerate by a median factor of 11, with faster rates on islands colonized in the past 1500 years than for those colonized earlier. This global anthropogenic acceleration in turnover suggests that islands are on trajectories of continuing change. Strategies for biodiversity conservation and ecosystem restoration must acknowledge the long duration of human impacts and the degree to which ecological changes today differ from prehuman dynamics.

Equids engineer desert water availability

Megafauna play important roles in the biosphere, yet little is known about how they shape dryland ecosystems. We report on an overlooked form of ecosystem engineering by donkeys and horses. In the deserts of North America, digging of ≤2-meter wells to groundwater by feral equids increased the density of water features, reduced distances between waters, and, at times, provided the only water present. Vertebrate richness and activity were higher at equid wells than at adjacent dry sites, and, by mimicking flood disturbance, equid wells became nurseries for riparian trees. Our results suggest that equids, even those that are introduced or feral, are able to buffer water availability, which may increase resilience to ongoing human-caused aridification.

Electric field control of natural optical activity in a multiferroic helimagnet

Controlling the chiral degree of freedom in matter has long been an important issue for many fields of science. The spin-spiral order, which exhibits a strong magnetoelectric coupling, gives rise to chirality irrespective of the atomic arrangement of matter. Here, we report the resonantly enhanced natural optical activity on the electrically active magnetic excitation, that is, electromagnon, in multiferroic cupric oxide. The electric field control of the natural optical activity is demonstrated through magnetically induced chirality endowed with magnetoelectric coupling. These optical properties inherent to multiferroics may lead to optical devices based on the control of chirality.

Atomic-scale ion transistor with ultrahigh diffusivity

Biological ion channels rapidly and selectively gate ion transport through atomic-scale filters to maintain vital life functions. We report an atomic-scale ion transistor exhibiting ultrafast and highly selective ion transport controlled by electrical gating in graphene channels around 3 angstroms in height, made from a single flake of reduced graphene oxide. The ion diffusion coefficient reaches two orders of magnitude higher than the coefficient in bulk water. Atomic-scale ion transport shows a threshold behavior due to the critical energy barrier for hydrated ion insertion. Our in situ optical measurements suggest that ultrafast ion transport likely originates from highly dense packing of ions and their concerted movement inside the graphene channels.

A risk-based approach for managing hydraulic fracturing-induced seismicity

Risks from induced earthquakes are a growing concern that needs effective management. For hydraulic fracturing of the Eagle Ford shale in southern Texas, we developed a risk-informed strategy for choosing red-light thresholds that require immediate well shut-in. We used a combination of datasets to simulate spatially heterogeneous nuisance and damage impacts. Simulated impacts are greater in the northeast of the play and smaller in the southwest. This heterogeneity is driven by concentrations of population density. Spatially varying red-light thresholds normalized on these impacts [moment magnitude (Mw) 2.0 to 5.0] are fairer and safer than a single threshold applied over a broad area. Sensitivity tests indicate that the forecast maximum magnitude is the most influential parameter. Our method provides a guideline for traffic light protocols and managing induced seismicity risks.

Parity-preserving and magnetic field-resilient superconductivity in InSb nanowires with Sn shells

Improving materials used to make qubits is crucial to further progress in quantum information processing. Of particular interest are semiconductor-superconductor heterostructures that are expected to form the basis of topological quantum computing. We grew semiconductor indium antimonide nanowires that were coated with shells of tin of uniform thickness. No interdiffusion was observed at the interface between Sn and InSb. Tunnel junctions were prepared by in situ shadowing. Despite the lack of lattice matching between Sn and InSb, a 15-nanometer-thick shell of tin was found to induce a hard superconducting gap, with superconductivity persisting in magnetic field up to 4 teslas. A small island of Sn-InSb exhibits the two-electron charging effect. These findings suggest a less restrictive approach to fabricating superconducting and topological quantum circuits.

A widespread pathway for substitution of adenine by diaminopurine in phage genomes

DNA modifications vary in form and function but generally do not alter Watson-Crick base pairing. Diaminopurine (Z) is an exception because it completely replaces adenine and forms three hydrogen bonds with thymine in cyanophage S-2L genomic DNA. However, the biosynthesis, prevalence, and importance of Z genomes remain unexplored. Here, we report a multienzyme system that supports Z-genome synthesis. We identified dozens of globally widespread phages harboring such enzymes, and we further verified the Z genome in one of these phages, Acinetobacter phage SH-Ab 15497, by using liquid chromatography with ultraviolet and mass spectrometry. The Z genome endows phages with evolutionary advantages for evading the attack of host restriction enzymes, and the characterization of its biosynthetic pathway enables Z-DNA production on a large scale for a diverse range of applications.

A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes

Cells have two purine pathways that synthesize adenine and guanine ribonucleotides from phosphoribose via inosylate. A chemical hybrid between adenine and guanine, 2-aminoadenine (Z), replaces adenine in the DNA of the cyanobacterial virus S-2L. We show that S-2L and Vibrio phage PhiVC8 encode a third purine pathway catalyzed by PurZ, a distant paralog of succinoadenylate synthase (PurA), the enzyme condensing aspartate and inosylate in the adenine pathway. PurZ condenses aspartate with deoxyguanylate into dSMP (N6-succino-2-amino-2'-deoxyadenylate), which undergoes defumarylation and phosphorylation to give dZTP (2-amino-2'-deoxyadenosine-5'-triphosphate), a substrate for the phage DNA polymerase. Crystallography and phylogenetics analyses indicate a close relationship between phage PurZ and archaeal PurA enzymes. Our work elucidates the biocatalytic innovation that remodeled a DNA building block beyond canonical molecular biology.

Noncanonical DNA polymerization by aminoadenine-based siphoviruses

Bacteriophage genomes harbor the broadest chemical diversity of nucleobases across all life forms. Certain DNA viruses that infect hosts as diverse as cyanobacteria, proteobacteria, and actinobacteria exhibit wholesale substitution of aminoadenine for adenine, thereby forming three hydrogen bonds with thymine and violating Watson-Crick pairing rules. Aminoadenine-encoded DNA polymerases, homologous to the Klenow fragment of bacterial DNA polymerase I that includes 3'-exonuclease but lacks 5'-exonuclease, were found to preferentially select for aminoadenine instead of adenine in deoxynucleoside triphosphate incorporation templated by thymine. Polymerase genes occur in synteny with genes for a biosynthesis enzyme that produces aminoadenine deoxynucleotides in a wide array of Siphoviridae bacteriophages. Congruent phylogenetic clustering of the polymerases and biosynthesis enzymes suggests that aminoadenine has propagated in DNA alongside adenine since archaic stages of evolution.

Structural impact on SARS-CoV-2 spike protein by D614G substitution

Substitution for aspartic acid (D) by glycine (G) at position 614 in the spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears to facilitate rapid viral spread. The G614 strain and its recent variants are now the dominant circulating forms. Here, we report cryo–electron microscopy structures of a full-length G614 S trimer, which adopts three distinct prefusion conformations that differ primarily by the position of one receptor-binding domain. A loop disordered in the D614 S trimer wedges between domains within a protomer in the G614 spike. This added interaction appears to prevent premature dissociation of the G614 trimer—effectively increasing the number of functional spikes and enhancing infectivity—and to modulate structural rearrangements for membrane fusion. These findings extend our understanding of viral entry and suggest an improved immunogen for vaccine development.

Toxin-antitoxin RNA pairs safeguard CRISPR-Cas systems

CRISPR-Cas systems provide RNA-guided adaptive immunity in prokaryotes. We report that the multisubunit CRISPR effector Cascade transcriptionally regulates a toxin-antitoxin RNA pair, CreTA. CreT (Cascade-repressed toxin) is a bacteriostatic RNA that sequesters the rare arginine tRNAUCU (transfer RNA with anticodon UCU). CreA is a CRISPR RNA–resembling antitoxin RNA, which requires Cas6 for maturation. The partial complementarity between CreA and the creT promoter directs Cascade to repress toxin transcription. Thus, CreA becomes antitoxic only in the presence of Cascade. In CreTA-deleted cells, cascade genes become susceptible to disruption by transposable elements. We uncover several CreTA analogs associated with diverse archaeal and bacterial CRISPR-cas loci. Thus, toxin-antitoxin RNA pairs can safeguard CRISPR immunity by making cells addicted to CRISPR-Cas, which highlights the multifunctionality of Cas proteins and the intricate mechanisms of CRISPR-Cas regulation.

Structural insights into preinitiation complex assembly on core promoters

Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)–mediated eukaryotic transcription. We determined the structures of human TFIID–based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA–TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)–activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.

Stepwise pathogenic evolution of Mycobacterium abscessus

Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria. We show that epigenetic modifiers, acquired through horizontal gene transfer, cause saltational increases in the pathogenic potential of specific environmental clones. Allopatric parallel evolution during chronic lung infection then promotes rapid increases in virulence through mutations in a discrete gene network; these mutations enhance growth within macrophages but impair fomite survival. As a consequence, we observe constrained pathogenic evolution while person-to-person transmission remains indirect, but postulate accelerated pathogenic adaptation once direct transmission is possible, as observed for M. tuberculosis. Our findings indicate how key interventions, such as early treatment and cross-infection control, might restrict the spread of existing mycobacterial pathogens and prevent new, emergent ones.

Chronoculture, harnessing the circadian clock to improve crop yield and sustainability

Human health is dependent on a plentiful and nutritious supply of food, primarily derived from crop plants. Rhythmic supply of light as a result of the day and night cycle led to the evolution of circadian clocks that modulate most plant physiology, photosynthesis, metabolism, and development. To regulate crop traits and adaptation, breeders have indirectly selected for variation at circadian genes. The pervasive impact of the circadian system on crops suggests that future food production might be improved by modifying circadian rhythms, engineering the timing of transgene expression, and applying agricultural treatments at the most effective time of day. We describe the applied research required to take advantage of circadian biology in agriculture to increase production and reduce inputs.

Modulation of MHC-E transport by viral decoy ligands is required for RhCMV/SIV vaccine efficacy

Strain 68-1 rhesus cytomegalovirus (RhCMV) vectors expressing simian immunodeficiency virus (SIV) antigens elicit CD8+ T cells recognizing epitopes presented by major histocompatibility complex II (MHC-II) and MHC-E but not MHC-Ia. These immune responses mediate replication arrest of SIV in 50 to 60% of monkeys. We show that the peptide VMAPRTLLL (VL9) embedded within the RhCMV protein Rh67 promotes intracellular MHC-E transport and recognition of RhCMV-infected fibroblasts by MHC-E–restricted CD8+ T cells. Deletion or mutation of viral VL9 abrogated MHC-E–restricted CD8+ T cell priming, resulting in CD8+ T cell responses exclusively targeting MHC-II–restricted epitopes. These responses were comparable in magnitude and differentiation to responses elicited by 68-1 vectors but did not protect against SIV. Thus, Rh67-enabled direct priming of MHC-E–restricted T cells is crucial for RhCMV/SIV vaccine efficacy.