The adaptation of the CRISPR-Cas9 system as a genome editing technique has generated much excitement in recent years owing to its ability to manipulate targeted genes and genomic regions that are ...complementary to a programmed single guide RNA (sgRNA). However, the efficacy of a specific sgRNA is not uniquely defined by exact sequence homology to the target site, thus unintended off-targets might additionally be cleaved. Current methods for sgRNA design are mainly concerned with predicting off-targets for a given sgRNA using basic sequence features and employ elementary rules for ranking possible sgRNAs. Here, we introduce CRISTA (CRISPR Target Assessment), a novel algorithm within the machine learning framework that determines the propensity of a genomic site to be cleaved by a given sgRNA. We show that the predictions made with CRISTA are more accurate than other available methodologies. We further demonstrate that the occurrence of bulges is not a rare phenomenon and should be accounted for in the prediction process. Beyond predicting cleavage efficiencies, the learning process provides inferences regarding patterns that underlie the mechanism of action of the CRISPR-Cas9 system. We discover that attributes that describe the spatial structure and rigidity of the entire genomic site as well as those surrounding the PAM region are a major component of the prediction capabilities.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
•The article models ridership impacts of integrating ridesourcing with public transit.•Ridesourcing can help promote transit ridership and reduce operation costs.•Ridesourcing complements public ...transit by enhancing last-mile transit access.•Ridesourcing significantly reduces the wait time and travel time of a transit trip.•Transfers and additional pickups deter the integration of ridesourcing and transit.
Inspired by the success of private ridesourcing companies such as Uber and Lyft, transit agencies have started to consider integrating ridesourcing services (i.e. on-demand, app-driven ridesharing services) with public transit. Ridesourcing services may enhance the transit system in two major ways: replacing underutilized routes to improve operational efficiency, and providing last-mile connectivity to extend transit’s catchment area. While an integrated system of ridesourcing services and public transit is conceptually appealing, little is known regarding whether and how consumers might use a system like this and what key service attributes matter the most to them. This article investigates traveler responses to a proposed integrated transit system, named MTransit, at the University of Michigan Ann Arbor campus. We conducted a large-sample survey to collect both revealed preference (RP) and stated preference (SP) data and fit a RP-SP mixed logit model to examine the main determinants of commuting mode choice. The model results show that transfers and additional pickups are major deterrents for MTransit use. We further applied the model outputs to forecast the demand for MTransit under different deployment scenarios. We find that replacing low-ridership bus lines with ridesourcing services could slightly increase transit ridership while reducing operations costs. The service improvements offered by ridesourcing mainly come from reductions in wait time. Though relatively small in our study, another source of improvement is the decrease of in-vehicle travel time. Moreover, we find that when used to provide convenient last-mile connections, ridesourcing could provide a significant boost to transit. This finding verifies a popular notion among transit professionals that ridesourcing services can serve as a complement to public transit by enhancing last-mile transit access.
Brown planthopper (BPH), white‐backed planthopper (WBPH) and small brown planthopper (SBPH), are the closely related rice pests that perform differentially on wheat plants. Using fecundity as a ...fitness measure, we found that SBPH well‐adapted on wheat plants, followed by WBPH, while BPH had the worst performance. The transcriptomic responses of SBPH and BPH to wheat plants have been compared previously. To understand the different fitness mechanisms of three planthoppers, this study first investigated the transcriptomic responses of WBPH to rice and wheat plants. Genes involved in detoxification, transportation and proteasome were significantly enriched in WBPH in response to different diets. Moreover, comparative analysis demonstrated that most co‐regulated genes in BPH and SBPH showed different expression changes; whereas most co‐regulated genes in BPH and WBPH exhibited similar expression changes. Subsequently, this study also investigated the influences of host plants on the bacterial community of three planthoppers. The three planthoppers harboured distant diversity of bacterial communities. However, there was no dramatic change in bacterial diversity or relative abundance in planthoppers colonized on different hosts. This study illustrates generic and species‐specific changes of three rice planthoppers in response to different plants, which deepen our understanding towards the host fitness for planthopper species.
The majority of co‐regulated genes changed similarly between BPH and WBPH, but reciprocally between SBPH and WBPH.
No dramatic change in bacterial community when planthoppers colonized on different hosts.
Host transfer frequency may account for the easier adaptation of SBPH to wheat plants than that of WBPH and BPH
The response to exercise training (trainability) has been shown to have a strong heritable component. There is growing evidence suggesting that traits such as trainability do not only depend on the ...genetic code, but also on epigenetic signals. Epigenetic signals play an important role in the modulation of gene expression, through mechanisms such as DNA methylation and histone modifications. There is an emerging evidence to show that physical activity influences DNA methylation in humans. The present review aims to summarize current knowledge on the link between DNA methylation and physical activity in humans. We have critically reviewed the literature and only papers focused on physical activity and its influence on DNA methylation status were included; a total of 25 papers were selected. We concluded that both acute and chronic exercises significantly impact DNA methylation, in a highly tissue‐ and gene‐specific manner. This review also provides insights into the molecular mechanisms of exercise‐induced DNA methylation changes, and recommendations for future research.
We report the experimental generation of highly energetic carbon ions up to 48 MeV per nucleon by shooting double-layer targets composed of well-controlled slightly underdense plasma and ultrathin ...foils with ultraintense femtosecond laser pulses. Particle-in-cell simulations reveal that carbon ions are ejected from the ultrathin foils due to radiation pressure and then accelerated in an enhanced sheath field established by the superponderomotive electron flow. Such a cascaded acceleration is especially suited for heavy ion acceleration with femtosecond laser pulses. The breakthrough of heavy ion energy up to many tens of MeV/u at a high repetition rate would be able to trigger significant advances in nuclear physics, high energy density physics, and medical physics.
Formal safety assessment (FSA), as a structured and systematic risk evaluation methodology, has been increasingly and broadly used in the shipping industry around the world. Concerns have been raised ...as to navigational safety of the Yangtze River, China's largest and the world's busiest inland waterway. Over the last few decades, the throughput of ships in the Yangtze River has increased rapidly due to the national development of the Middle and Western parts of China. Accidents such as collisions, groundings, contacts, oil-spills and fires occur repeatedly, often causing serious consequences. In order to improve the navigational safety in the Yangtze River, this paper estimates the navigational risk of the Yangtze River using the FSA concept and a Bayesian network (BN) technique. The navigational risk model is established by considering both probability and consequences of accidents with respect to a risk matrix method, followed by a scenario analysis to demonstrate the application of the proposed model.
Bacterial class 2 CRISPR-Cas systems utilize a single RNA-guided protein effector to mitigate viral infection. We aggregated genomic data from multiple sources and constructed an expanded database of ...predicted class 2 CRISPR-Cas systems. A search for novel RNA-targeting systems identified subtype VI-D, encoding dual HEPN domain-containing Cas13d effectors and putative WYL-domain-containing accessory proteins (WYL1 and WYL-b1 through WYL-b5). The median size of Cas13d proteins is 190 to 300 aa smaller than that of Cas13a–Cas13c. Despite their small size, Cas13d orthologs from Eubacterium siraeum (Es) and Ruminococcus sp. (Rsp) are active in both CRISPR RNA processing and targeting, as well as collateral RNA cleavage, with no target-flanking sequence requirements. The RspWYL1 protein stimulates RNA cleavage by both EsCas13d and RspCas13d, demonstrating a common regulatory mechanism for divergent Cas13d orthologs. The small size, minimal targeting constraints, and modular regulation of Cas13d effectors further expands the CRISPR toolkit for RNA manipulation and detection.
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•Type VI-D is a CRISPR-Cas system with a Cas13d effector and a WYL domain accessory•Cas13d is an RNA-guided RNase approximately 20% smaller than Cas13a–Cas13c effectors•WYL1 positively modulates Cas13d target and collateral RNase activity•Cas13d has minimal sequence and secondary structure requirements for targeting
Compiling an expanded database of predicted class 2 CRISPR-Cas systems, Yan et al. identify and characterize subtype VI-D. Cas13d is an RNA-guided RNase effector with polyphyletic WYL-domain accessory proteins. One WYL1 ortholog enhances activity of divergent Cas13d orthologs. The small effector size and modular enhancement further expand RNA modification capabilities.
Elastic electron-proton scattering (e-p) and the spectroscopy of hydrogen atoms are the two methods traditionally used to determine the proton charge radius, r
. In 2010, a new method using muonic ...hydrogen atoms
found a substantial discrepancy compared with previous results
, which became known as the 'proton radius puzzle'. Despite experimental and theoretical efforts, the puzzle remains unresolved. In fact, there is a discrepancy between the two most recent spectroscopic measurements conducted on ordinary hydrogen
. Here we report on the proton charge radius experiment at Jefferson Laboratory (PRad), a high-precision e-p experiment that was established after the discrepancy was identified. We used a magnetic-spectrometer-free method along with a windowless hydrogen gas target, which overcame several limitations of previous e-p experiments and enabled measurements at very small forward-scattering angles. Our result, r
= 0.831 ± 0.007
± 0.012
femtometres, is smaller than the most recent high-precision e-p measurement
and 2.7 standard deviations smaller than the average of all e-p experimental results
. The smaller r
we have now measured supports the value found by two previous muonic hydrogen experiments
. In addition, our finding agrees with the revised value (announced in 2019) for the Rydberg constant
-one of the most accurately evaluated fundamental constants in physics.
Precisely measuring the location and frequency of DNA double-strand breaks (DSBs) along the genome is instrumental to understanding genomic fragility, but current methods are limited in versatility, ...sensitivity or practicality. Here we present Breaks Labeling In Situ and Sequencing (BLISS), featuring the following: (1) direct labelling of DSBs in fixed cells or tissue sections on a solid surface; (2) low-input requirement by linear amplification of tagged DSBs by in vitro transcription; (3) quantification of DSBs through unique molecular identifiers; and (4) easy scalability and multiplexing. We apply BLISS to profile endogenous and exogenous DSBs in low-input samples of cancer cells, embryonic stem cells and liver tissue. We demonstrate the sensitivity of BLISS by assessing the genome-wide off-target activity of two CRISPR-associated RNA-guided endonucleases, Cas9 and Cpf1, observing that Cpf1 has higher specificity than Cas9. Our results establish BLISS as a versatile, sensitive and efficient method for genome-wide DSB mapping in many applications.
•A novel Zn-MOF with unique structure was synthesized and characterized.•The structure of the MOF consists of pinwheel trinuclear clusters and 3D pillar-layeres.•The synthesized MOF was used as a ...precursor for preparation of ZnO.
A novel metal-organic frameworks (MOF), namely ({Zn3(2,6-NDC)3(dabco)·6DMF·3H2O} (TMU-13) was synthesized by the reaction of 2,6-naphthalenedicarboxylic acid (2,6-NDC) as the O-donor ligand, 1,4-diazabicyclo 2.2.2 octane (dabco) as the N-donor ligand and Zn(II) nitrate hexahydrate. Single crystal X-ray analysis revealed that TMU-13 exhibited a 3D pillar-layered structure based on pinwheel trinuclear zinc-carboxylate clusters as secondary building unit (SBU) with bcu topology and pore window of 12.7 Å × 5.6 Å. Calcination of the compounds TMU-13 at 500 °C under air atmosphere yield ZnO compound.
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