Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity
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Biochemistry & Molecular Biology↗
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PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease
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Yang, Hui↗
Brachiopod δ 34 S CAS microanalyses indicate a dynamic, climate-influenced Permo-Carboniferous sulfur cycle
Early isotopic studies of sulfate in carbonate minerals (carbonate associated sulfate; CAS) suggested that carbonates can provide a reliable, well-dated archive of the marine sulfur cycle through time. However, subsequent research has shown that diagenetic alteration can impose highly heterogeneous CAS sulfur isotopic compositions (δ 34 S CAS ) among different carbonate phases within sediments. Such alteration necessitates targeted sampling of well-preserved, primary carbonate phases. Here, we present a new record of Carboniferous and Early Permian brachiopod δ 34 S CAS generated from over 130 measurements of microsampled brachiopod shells. Our record refines existing brachiopod δ 34 S CAS records and confirms a large, ~6.5‰ δ 34 S CAS decrease in the Early Carboniferous. Importantly, the record also features a novel 3–5‰ increase in δ 34 S CAS near the Serpukhovian-Bashkirian boundary (323.4 Ma) that coincides with carbonate δ 13 C and δ 18 O increases. Variability in δ 34 S CAS is minor both within (≤0.3‰) and among (≤2‰) individual co-depositional brachiopod specimens. A taxon-specific δ 34 S CAS offset is present one species (Composita subtilita) that also exhibits a δ 13 C offset, supporting the existence of biological “vital effects” on δ 34 S CAS . Geologic evidence and mathematical modeling of the Permo-Carboniferous carbon and sulfur cycles suggest that changes in the burial ratio of organic carbon to pyrite sulfur (R C:S ) are insufficient to explain the observed mid-Carboniferous δ 34 S CAS record. We find that changes in the 34 S depletion of pyrite relative to seawater sulfate ( 34 ε) or in the δ 34 S of the input to the ocean (δ 34 S in ) are also needed. Large additions of O 2 from organic carbon burial during the Permo-Carboniferous cannot be entirely compensated for with sulfur cycle changes; lower than modern late Visean pO 2 and/or additional O 2 sinks are needed to keep pO 2 at plausible levels. Based on the geologic context surrounding our record's mid-Carboniferous δ 34 S CAS increase, we advocate for simultaneous changes in pyrite burial, 34 ε, and δ 34 S in , driven by sea level or tectonically induced changes in environments of sulfur burial, as a viable mechanism to produce rapid seawater δ 34 S changes.
54 ENVIRONMENTAL SCIENCES↗
Expression of cellular apoptosis susceptibility (CAS) in the human testis and testicular germ cell tumors
Testicular germ cell tumors are the most frequent malignancies found in men between 15 and 44 years old. Although cellular apoptosis susceptibility (CAS) was demonstrated to be upregulated in breast cancer and colon cancer, the expression of CAS in the human testis and testicular germ cell tumors remained elusive. In the present study, CAS-positive signals were detected in the normal testicular tissues, cancer adjacent normal testicular tissues, seminoma, yolk sac tumor, and teratoma. Interestingly, the expression level of CAS in testicular germ cell tumors (TGCTs) (but not seminoma) was significantly lower than that of human testicular tissues and cancer adjacent normal testicular tissues, suggesting that decreased CAS contributed to the progression of TGCTs. Notably, the expression of CAS in seminoma was significantly higher than that of in the non-seminomas, consistent with the results from TCGA database. Furthermore, the localization of CAS is mainly restricted in the nucleus in the lesions of normal human testicular tissue and cancer adjacent normal testicular tissue. Although the expression of CAS was not significantly different between normal testicular tissue and seminoma, CAS was more enriched in cytoplasm in seminoma compared to the normal, cancer adjacent tissue and other types of TGCTs. The current results demonstrated reduced expression of CAS in the human testicular germ cell tumors and the CAS translocation from the nuclear to cytoplasm in seminoma, thereby supporting a possible role in normal testis function and in the development of seminoma.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires
Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, the cas1 gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium— Arthrospira platensis . Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse pool but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown. IMPORTANCE While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic. While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures of Arthrospira platensis , a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.
horizontal gene transfer↗
DISTANCE AND PROPER MOTION MEASUREMENT OF THE RED SUPERGIANT, PZ CAS, IN VERY LONG BASELINE INTERFEROMETRY H{sub 2}O MASER ASTROMETRY
We present the very long baseline interferometry H{sub 2}O maser monitoring observations of the red supergiant, PZ Cas, at 12 epochs from 2006 April to 2008 May. We fitted maser motions to a simple model composed of a common annual parallax and linear motions of the individual masers. The maser motions with the parallax subtracted were well modeled by a combination of a common stellar proper motion and a radial expansion motion of the circumstellar envelope. We obtained an annual parallax of 0.356 {+-} 0.026 mas and a stellar proper motion of {mu}{sub {alpha}}{sup *} cos {delta} = -3.7 {+-} 0.2 and {mu}{sup *}{sub {delta}}=-2.0{+-}0.3 mas yr{sup -1} eastward and northward, respectively. The annual parallax corresponds to a trigonometric parallax of 2.81{sup +0.22}{sub -0.19} kpc. By rescaling the luminosity of PZ Cas in any previous studies using our trigonometric parallax, we estimated the location of PZ Cas on a Hertzsprung-Russell diagram and found that it approaches a theoretically evolutionary track around an initial mass of {approx}25 M{sub Sun }. The sky position and the distance to PZ Cas are consistent with the OB association, Cas OB5, which is located in a molecular gas super shell. The proper motion of PZ Cas is close to that of the OB stars and other red supergiants in Cas OB5 measured by the Hipparcos satellite. We derived the peculiar motion of PZ Cas of U{sub s} = 22.8 {+-} 1.5, V{sub s} = 7.1 {+-} 4.4, and W{sub s} = -5.7 {+-} 4.4 km s{sup -1}. This peculiar motion has rather a large U{sub s} component, unlike those of near high-mass star-forming regions with negatively large V{sub s} motions. The uniform proper motions of the Cas OB5 member stars suggest random motions of giant molecular clouds moving into local potential minima in a time-dependent spiral arm, rather than a velocity field caused by the spiral arm density wave.
79 ASTRONOMY AND ASTROPHYSICS↗
Spacer2PAM: A computational framework to guide experimental determination of functional CRISPR-Cas system PAM sequences
Abstract RNA-guided nucleases from CRISPR-Cas systems expand opportunities for precise, targeted genome modification. Endogenous CRISPR-Cas systems in many prokaryotes are attractive to circumvent expression, functionality, and unintended activity hurdles posed by heterologous CRISPR-Cas effectors. However, each CRISPR-Cas system recognizes a unique set of protospacer adjacent motifs (PAMs), which requires identification by extensive screening of randomized DNA libraries. This challenge hinders development of endogenous CRISPR-Cas systems, especially those based on multi-protein effectors and in organisms that are slow-growing or have transformation idiosyncrasies. To address this challenge, we present Spacer2PAM, an easy-to-use, easy-to-interpret R package built to predict and guide experimental determination of functional PAM sequences for any CRISPR-Cas system given its corresponding CRISPR array as input. Spacer2PAM can be used in a ‘Quick’ method to generate a single PAM prediction or in a ‘Comprehensive’ method to inform targeted PAM libraries small enough to screen in difficult to transform organisms. We demonstrate Spacer2PAM by predicting PAM sequences for industrially relevant organisms and experimentally identifying seven PAM sequences that mediate interference from the Spacer2PAM-informed PAM library for the type I-B CRISPR-Cas system from Clostridium autoethanogenum. We anticipate that Spacer2PAM will facilitate the use of endogenous CRISPR-Cas systems for industrial biotechnology and synthetic biology.
59 BASIC BIOLOGICAL SCIENCES↗
New CRISPR–Cas systems from uncultivated microbes
We present that CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped. Metagenomics, the sequencing of DNA extracted directly from natural microbial communities, provides access to the genetic material of a huge array of uncultivated organisms. Here, using genome-resolved metagenomics, we identify a number of CRISPR-Cas systems, including the first reported Cas9 in the archaeal domain of life, to our knowledge. This divergent Cas9 protein was found in little-studied nanoarchaea as part of an active CRISPR-Cas system. In bacteria, we discovered two previously unknown systems, CRISPR-CasX and CRISPR-CasY, which are among the most compact systems yet discovered. Notably, all required functional components were identified by metagenomics, enabling validation of robust in vivo RNA-guided DNA interference activity in Escherichia coli. Lastly, interrogation of environmental microbial communities combined with in vivo experiments allows us to access an unprecedented diversity of genomes, the content of which will expand the repertoire of microbe-based biotechnologies.
59 BASIC BIOLOGICAL SCIENCES↗
CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes
Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
59 BASIC BIOLOGICAL SCIENCES↗
Poster — Thur Eve — 36: Implementation of constant dose rate and gantry speed arc therapy(CDR-CAS-IMAT) for thoracic esophageal carcinoma on Varian 23EX
Objective: The purpose of this study is to propose an alternative planning approach for VMAT using constant dose rate and gantry speed arc therapy(CDR-CAS-IMAT) implementation on conventional Linac Varian 23EX and used IMRT as a benchmark to evaluate the performance. Methods and materials: Eighteen patients with thoracic esophageal carcinoma who were previously treated with IMRT on Varian 23EX were retrospectively planned for CDR-CAS-IMAT plans. Dose prescription was set to 60 Gy to PTVs in 30 fractions. The planning objectives for PTVs and OAR were corresponding with the IMRT plans. Dose to the PTVs and OAR were compared to IMRT with respect to plan quality, MU, treatment time and delivery accuracy. Results: CDR-CAS-IMAT plans led to equivalent or superior plan quality as compared to IMRT, PTV's CI relative increased 16.2%, while small deviations were observed on minimum dose for PTV. Volumes in the cord receiving 40Gy were increased from 3.6% with IMRT to 7.0%. Treatment times were reduced significantly with CDR-CAS-IMAT(mean 85.7s vs. 232.1s, p < .05), however, MU increased by a factor of 1.3 and lung V10/5/3.5/aver were relative increase 6.7%,12%,17.9%,4.2%, respectively. And increased the E-P low dose area volume decreased the hight dose area. There were no significant difference in Delta4 measurements results between both planning techniques. Conclusion: CDR-CAS-IMAT plans can be implemented smoothly and quickly into a busy cancer center, which improved PTV CI and reduces treatment time but increased the MU and low dose irradiated area. An evaluation of weight loss must be performed during treatment for CDR-CAS-IMAT patients.
60 APPLIED LIFE SCIENCES↗
Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming
Abstract There is an increasing interest in the clustered regularly interspaced short palindromic repeats CRISPR-associated protein (CRISPR-Cas) system to reveal potential virus–host dynamics. The universal and most conserved Cas protein, cas1 is an ideal marker to elucidate CRISPR-Cas ecology. We constructed eight Hidden Markov Models (HMMs) and assembled cas1 directly from metagenomes by a targeted-gene assembler, Xander, to improve detection capacity and resolve the diverse CRISPR-Cas systems. The eight HMMs were first validated by recovering all 17 cas1 subtypes from the simulated metagenome generated from 91 prokaryotic genomes across 11 phyla. We challenged the targeted method with 48 metagenomes from a tallgrass prairie in Central Oklahoma recovering 3394 cas1. Among those, 88 were near full length, 5 times more than in de-novo assemblies from the Oklahoma metagenomes. To validate the host assignment by cas1, the targeted-assembled cas1 was mapped to the de-novo assembled contigs. All the phylum assignments of those mapped contigs were assigned independent of CRISPR-Cas genes on the same contigs and consistent with the host taxonomies predicted by the mapped cas1. We then investigated whether 8 years of soil warming altered cas1 prevalence within the communities. A shift in microbial abundances was observed during the year with the biggest temperature differential (mean 4.16 °C above ambient). cas1 prevalence increased and even in the phyla with decreased microbial abundances over the next 3 years, suggesting increasing virus–host interactions in response to soil warming. This targeted method provides an alternative means to effectively mine cas1 from metagenomes and uncover the host communities.
54 ENVIRONMENTAL SCIENCES↗
SU-E-P-55: The Reaserch of Cervical Cancer Delivered with Constant Dose Rate and Gantry Speed Arc Therapy(CDR-CAS-IMAT) On Conventional Linac
Purpose: Postoperative cervical cancer patients with large target volume and the target shape is concave, treatmented with static intensity-modulated radiotherapy (IMRT) is time consuming. The purpose of this study is to investigate using constant dose rate and gantry speed arc therapy(CDR-CAS-IMAT) on conventional linear accelrator, by comparing with the IMRT technology to evaluate the performance of CDR-CAS-IMAT on postoperative cervical cancer patients. Methods: 18 cervical cancer patients treated with IMRT on Varian 23IX were replanted using CDR-CAS-IMAT. The plans were generated on Oncentra v4.1 planning system, PTV was prescribed to 50.4 Gy in 28 fractions. Plans were evaluated based on the ability to meet the dose volume histogram. The homogeneity index (HI), conformity index (CI) of target volume, the dose of organs at risk, radiation delivery time and monitor units were also compared. SPSS 19.0 software paired T-test analysis was carried out on the two sets of data. Results: Compared with the IMRT plans PTV’s CI (t= 3.85, P =0.001), CTV’s CI, HI, D90, D95, D98, V95, V98, V100 (t=4.21, −3.18, 2.13, 4.65, 7.79, 2.29, 6.00, 2.13, p=0.001, 0.005, 0.049, 0.000, 0.000, 0.035, 0.000, 0.049), and cord D2 and rectum V40 (t=−2.65, −2.47, p= P =0.017, 0.025), and treatment time and MU (t=−36.0, −6.26, P =0.000, 0.000) were better than that of IMRT group. But the IMRT plans in terms of decreasing bladder V50, bowel V30 (t=2.14, 3.00, P =0.048, 0.008) and low dose irradiation volume were superior to that of CDR-CAS-IMAT plans. There were no significant differences in other statistical index. Conclusion: Cervical cancer patients with CDR-CAS-IMAT on Varian Clinical 23IX can get equivalent or superior dose distribution compared with the IMRT technology. IMAT have much less treatment time and MU can reduce the uncertainty factor and patient discomfort in treatment. This work was supported by the Medical Science Foundation of the health department of Hebei Province (No. 20130253)
60 APPLIED LIFE SCIENCES↗
CRISPR-Cas systems in the marine actinomycete Salinispora: linkages with phage defense, microdiversity and biogeography
Background: Prokaryotic CRISPR-Cas systems confer resistance to viral infection and thus mediate bacteria-phage interactions. However, the distribution and functional diversity of CRISPRs among environmental bacteria remains largely unknown. Here, comparative genomics of 75 Salinispora strains provided insight into the diversity and distribution of CRISPR-Cas systems in a cosmopolitan marine actinomycete genus. Results: CRISPRs were found in all Salinispora strains, with the majority containing multiple loci and different Cas array subtypes. Of the six subtypes identified, three have not been previously described. A lower prophage frequency in S. arenicola was associated with a higher fraction of spacers matching Salinispora prophages compared to S. tropica, suggesting differing defensive capacities between Salinispora species. The occurrence of related prophages in strains from distant locations, as well as spacers matching those prophages inserted throughout spacer arrays, indicate recurring encounters with widely distributed phages over time. Linkages of CRISPR features with Salinispora microdiversity pointed to subclade-specific contacts with mobile genetic elements (MGEs). This included lineage-specific spacer deletions or insertions, which may reflect weak selective pressures to maintain immunity or distinct temporal interactions with MGEs, respectively. Biogeographic patterns in spacer and prophage distributions support the concept that Salinispora spp. encounter localized MGEs. Moreover, the presence of spacers matching housekeeping genes suggests that CRISPRs may have functions outside of viral defense. Conclusions: This study provides a comprehensive examination of CRISPR-Cas systems in a broadly distributed group of environmental bacteria. The ubiquity and diversity of CRISPRs in Salinispora suggests that CRISPR-mediated interactions with MGEs represent a major force in the ecology and evolution of this cosmopolitan marine actinomycete genus.
54 ENVIRONMENTAL SCIENCES↗
Green Emitting Cerium Doped CaS Whiskers Grown by Solid State Diffusion Method
Undoped and cerium doped Calcium sulfide (CaS) phosphors were synthesized using solid state diffusion method. The X-ray diffraction pattern revealed that both undoped and doped CaS crystallites have cubic structure with average crystallite size varying from 20 to 30 nm. Scanning electron micrographs indicated that Ce doped CaS phosphors were composed of whiskers with different dimensions and orientations. The optical properties of undoped and Ce doped particles were characterized using Photoluminescence (PL) and UV-Vis absorption spectroscopy. The PL emission spectrum of cerium doped CaS phosphors for an excitation wavelength 465 nm showed a main peak at 500 nm and a shoulder peak at 556 nm due to 5d → 4f transition in Ce{sup 3+} ions. The variation of PL intensity with cerium concentration was investigated and the maximum PL intensity was obtained for a doping concentration of 3 wt.%. The optical band gap of the samples was estimated from the diffuse reflectance spectrum and was found to increase with increase in cerium concentration. The enhanced optical properties of these phosphors can be exploited in various optoelectronic devices including displays and bioimaging techniques.
36 MATERIALS SCIENCE↗
Spacer Acquisition Rates Determine the Immunological Diversity of the Type II CRISPR-Cas Immune Response
CRISPR-Cas systems provide acquired immunity in prokaryotes. Upon infection, short sequences from the phage genome, known as spacers, are inserted between the CRISPR repeats. Spacers are transcribed into small RNA molecules that guide nucleases to their targets. The forces that shape the distribution of newly acquired spacers, which is observed to be uneven, are poorly understood. We studied the spacer patterns that arise after phage infection of Staphylococcus aureus harboring the Streptococcus pyogenes type II-A CRISPR-Cas system. We observed that spacer patterns are established early during the CRISPR-Cas immune response and correlate with spacer acquisition rates, but not with spacer targeting efficiency. The rate of spacer acquisition depended on sequence elements within the spacer, which in turn determined the abundance of different spacers within the adapted population. Finally, our results reveal how the two main forces of the CRISPR-Cas immune response, acquisition and targeting, affect the generation of immunological diversity.
59 BASIC BIOLOGICAL SCIENCES↗
Selective Sorbent Design: CaS Aerogel for Rapid Remediation of Aqueous Pb (II)
Heavy metals are a persistent environmental problem due to their high toxicity, even at very low concentrations (parts per billion, ppb). The removal of such diluted heavy metals is challenging because of the competition the counterions (Ca 2+ , Na + , Mg 2+ , etc.) present in natural water bodies. The design of sorbents capable of removing ions below the action limit (15 ppb for Pb 2+ ) requires a strong driving force for selective uptake and rapid removal. In this work, we report the synthesis of porous CaS aerogels (surface area = 143.6 m 2 /g) by oxidative assembly of CaS nanoparticles and describe their use in selective Pb 2+ ion remediation from water. Despite the presence of amorphous CaCO 3 (up to 50 wt %) in the gel network, the gels demonstrated a capacity of 17.1 mmol Pb/g aerogel (3543 mg/g), and this could be augmented to 22.5 mmol Pb/g aerogel (4593 mg/g) by modifying the synthesis to reduce CaCO 3 content to ca. 15 wt %. Moreover, the selectivity of CaS aerogels toward Pb 2+ ions is high, as evidenced by little-to-no change in the distribution constant (K d ∼ 10 4 ) in the presence of competing ions (1 M) such as Na + , Mg 2+ , and Ca 2+ . During remediation with low concentrations (100 ppb) of Pb 2+ with CaS aerogels, the level of Pb 2+ dropped to 5.4 ppb (below the 15 ppb EPA limit) within 1 h with a 95.4% removal efficiency. In contrast to the CO 2 supercritically dried aerogels, lower surface area ambient dried gels (xerogels) only remove 40% of the lead ions from a 100 ppb solution, saturating within 1 h. The efficiency and rapidity of selective Pb 2+ uptake using CdS aerogels arise from a combination of a strong thermodynamic driving force for cation exchange (K eq = 2.5 × 10 27 ) and chemisorption along with favorable kinetics associated with the high surface area porous architecture. These results show that formation of high surface area metal chalcogenide aerogels by oxidative assembly to form nanocrystalline architectures, as previously demonstrated for II−VI and IV−VI semiconductors, can be extended to the more highly ionic alkaline earth sulfides.
Aerogels↗
Implementation of an Orographic Drag Scheme Considering Orographic Anisotropy in All Flow Directions in the Earth System Model CAS‐ESM 2.0
Abstract A reasonable representation of orographic anisotropy in earth system models is vital for improving weather and climate modeling. In this study, we implement the orographic drag scheme, including 3‐D orographic anisotropy (3D‐AFD), into the Chinese Academy of Sciences Earth System Model version 2 (CAS‐ESM 2.0). Three groups of simulations named sensitivity run, medium‐range forecast, and seasonal forecast respectively are conducted using the updated CAS‐ESM model and validated against station observation and reanalysis data. These simulations are run using the three schemes—3D‐AFD scheme, the 3D orographic anisotropy scheme for the eight‐direction (3D‐8x), and the 2D isotropic scheme (2D)—to compare their performance in CAS‐ESM 2.0. Sensitivity runs show that the 3D‐AFD provide more continuous transition of calculated drag as function of wind direction than the 3D‐8x, while the drag calculated using the 2D scheme show no variation with change of wind direction. Enhanced drag in the medium range and seasonal forecast using the updated CAS‐ESM alleviates part of the winter wind speed bias over the Tibetan Plateau (TP) and the cold bias over TP and the Siberian polar region. It is shown that the 3D‐AFD scheme alleviates more bias than that of the 3D‐8x scheme (by wind speed reduction of 1 ∼ 2 m/s and temperature of 1 ∼ 2 K) especially in the seasonal forecast. The results suggest that reasonable representation of the orographic anisotropy is important in climate modeling.
Xie, Jinbo↗
Inhibition mechanisms of AcrF9, AcrF8, and AcrF6 against type I-F CRISPR–Cas complex revealed by cryo-EM
Prokaryotes and viruses have fought a long battle against each other. Prokaryotes use CRISPR–Cas-mediated adaptive immunity, while conversely, viruses evolve multiple anti-CRISPR (Acr) proteins to defeat these CRISPR–Cas systems. The type I-F CRISPR–Cas system in Pseudomonas aeruginosa requires the crRNA-guided surveillance complex (Csy complex) to recognize the invading DNA. Although some Acr proteins against the Csy complex have been reported, other relevant Acr proteins still need studies to understand their mechanisms. As such, here, we obtain three structures of previously unresolved Acr proteins (AcrF9, AcrF8, and AcrF6) bound to the Csy complex using electron cryo-microscopy (cryo-EM), with resolution at 2.57 Å, 3.42 Å, and 3.15 Å, respectively. The 2.57-Å structure reveals fine details for each molecular component within the Csy complex as well as the direct and water-mediated interactions between proteins and CRISPR RNA (crRNA). Our structures also show unambiguously how these Acr proteins bind differently to the Csy complex. AcrF9 binds to key DNA-binding sites on the Csy spiral backbone. AcrF6 binds at the junction between Cas7.6f and Cas8f, which is critical for DNA duplex splitting. AcrF8 binds to a distinct position on the Csy spiral backbone and forms interactions with crRNA, which has not been seen in other Acr proteins against the Csy complex. Our structure-guided mutagenesis and biochemistry experiments further support the anti-CRISPR mechanisms of these Acr proteins. Our findings support the convergent consequence of inhibiting degradation of invading DNA by these Acr proteins, albeit with different modes of interactions with the type I-F CRISPR–Cas system.
59 BASIC BIOLOGICAL SCIENCES↗