Synergizing Off-Target Predictions for In Silico Insights of CENH3 Knockout in Cannabis through CRISPR/Cas

The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas-mediated genome editing system has recently been used for haploid production in plants. Haploid induction using the CRISPR/Cas system represents an attractive approach in cannabis, an economically important industrial, recreational, and medicinal plant. However, the CRISPR system requires the design of precise (on-target) single-guide RNA (sgRNA). Therefore, it is essential to predict off-target activity of the designed sgRNAs to avoid unexpected outcomes. The current study is aimed to assess the predictive ability of three machine learning (ML) algorithms (radial basis function (RBF), support vector machine (SVM), and random forest (RF)) alongside the ensemble-bagging (E-B) strategy by synergizing MIT and cutting frequency determination (CFD) scores to predict sgRNA off-target activity through in silico targeting a histone H3-like centromeric protein, HTR12, in cannabis. The RF algorithm exhibited the highest precision, recall, and F-measure compared to all the tested individual algorithms with values of 0.61, 0.64, and 0.62, respectively. We then used the RF algorithm as a meta-classifier for the E-B method, which led to an increased precision with an F-measure of 0.62 and 0.66, respectively. The E-B algorithm had the highest area under the precision recall curves (AUC-PRC; 0.74) and area under the receiver operating characteristic (ROC) curves (AUC-ROC; 0.71), displaying the success of using E-B as one of the common ensemble strategies. This study constitutes a foundational resource of utilizing ML models to predict gRNA off-target activities in cannabis.     

Metal Trimethylsilylthiolates for the Synthesis of Trinuclear MnPd2 Complexes

The manganese(II)‐palladium(II)‐sulfide complex [MnCl₂(μ₃‐S)₂Pd₂(dppp)₂] ( 2 ) was prepared from the reaction of [PdCl₂(dppp)] with [Li(N,N'‐tmeda)]₂[Mn(SSiMe₃)₄] ( 2 ) in a 2:1 ratio under mild conditions. The new trimethylsilylthiolate complex [Pd(dppp)(SSiMe₃)₂] ( 3 ) was synthesized from the reaction of [Pd(dppp)(OAc)₂] with two equivalents of Li[SSiMe₃]; this was then used in a reaction with [Mn(CH₃CN)₂(OTf)₂] to form the manganese(II)‐palladium(II)‐sulfide cluster [Mn(OTf)(thf)₂(μ₃‐S)₂Pd₂(dppp)₂]OTf ( 4 ).     

Catalytic performance in 4-nitrophenol reduction by Ag nanoparticles stabilized on biodegradable amphiphilic copolymers

Biodegradable copolymers have received much more attention in the last decades due their potential applications in the fields related to environmental protection, medicine, agriculture, and the chemical processes. Silver nanoparticles (Ag NPs) were prepared via reduction of silver nitrate (AgNO₃) using biodegradable amphiphilic copolymers in aqueous solution. The micelles were constructed from the amphiphilic copolymer composed of poly(2-ethyl-2-oxazoline) and poly(ε-caprolactone). The Ag NPs with a diameter of 10–15?nm were found to show a comparable high catalytic activity toward the reduction of 4-nitrophenol (4-NP) in the presence of an excess amount of NaBH₄. The synthesized Ag NPs-loaded copolymer exhibits high catalytic activity for the reduction of 4-NP to 4-aminophenol.     

An efficient biosurfactant-producing bacterium Pseudomonas aeruginosa MR01, isolated from oil excavation areas in south of Iran

A bacterial strain was isolated and cultured from the oil excavation areas in tropical zone in southern Iran. It was affiliated with Pseudomonas. The biochemical characteristics and partial sequenced 16S rRNA gene of isolate, MR01, was identical to those of cultured representatives of the species Pseudomonas aeruginosa. This bacterium was able to produce a type of biosurfactant with excessive foam-forming properties. Compositional analysis revealed that the extracted biosurfactant was composed of high percentages lipid (65%, w/w) and carbohydrate (30%, w/w) in addition to a minor fraction of protein (4%, w/w). The best production of 2.1 g/l was obtained when the cells were grown on minimal salt medium containing 1.2% (w/v) glucose and 0.1% (w/v) ammonium sulfate supplemented with 0.1% (w/v) isoleucine at 37 °C and 180 rpm after 2 days. The optimum biosurfactant production pH value was found to be 8.0. The MR01 could reduce surface tension to 28 mN/m and emulsified hexadecane up to E24  70. The results obtained from time course study indicated that the surface tension reduction and emulsification potential was increased in the same way to cell growth. However, maximum biosurfactant production occurred and established in the stationary growth phase (after 84 h). Fourier Transform Infrared spectrum of extracted biosurfactant indicates the presence of carboxyl, amine, hydroxyl and methoxyl functional groups. Thermogram of biosurfactant demonstrated three sharp endothermic peaks placing between 200 and 280 °C. The core holder flooding experiments demonstrated that the oil recovery efficiencies varied from 23.7% to 27.1% of residual oil.     

Relative wavefunctions, vertex functions and coupling constants for the virtual decay of 4He

The d + d, t + p and h + n relative wavefunctions and their asymptotic normalizations are considered in the framework of the generator coordinate method (GCM) and compared with ATMS (amalgamation of two-body correlation into multiple scattering processes) method which used the realistic Reid soft core interaction. The asymptotic normalization of relative wavefunctions provide various coupling constants, the cluster probability amplitude (the so-called Z ^1/2-factor) and matter RMS radii. These wavefunctions are also used to obtain ⁴He − d − d, ⁴He − t − p and ⁴He − h − n vertex functions in the virtual decay of ⁴He. The extrapolation of vertex functions for negative values of q ² upto the corresponding poles provide the vertex constants which are comparable with other estimates. It is noticed that in GCM the coupling constants C ² for ⁴He − d − d vertex is less than 2 as has been obtained in the forward dispersion relation technique.     

Quasielastic reactions around the coulomb barrier in 16O+118Sn

Measurement of elastic and quasielastic reaction cross sections were done in ¹⁶O + ¹¹⁸Sn system at two different energies above the barrier. Attempts are being made to understand the results in the framework of coupled reaction channel model.     

Interfacial segregation in Ag-Au,Au-Pd,and Cu-Ni alloys: II. [001] Σ5 twist grain boundaries

Atomistic simulations of segregation to [001] 5 twist boundaries in Cu–Ni, Au–Pd, and Ag–Au alloy systems have been performed for a wide range of temperatures and compositions within the solid solution region of these alloy phase diagrams. In addition to the grain boundary segregation profiles, grain boundary free energies, enthalpies, and entropies were determined. These simulations were performed within the framework of the free energy simulation method, in which an approximate free energy functional is minimized with respect to atomic coordinates and atomic site occupation. For all alloy bulk compositions (0.05 C 0.95) and temperatures (400 T (K) 1,100) examined, Cu and Au segregates to the boundary in the Cu–Ni and Au–Pd alloy systems, respectively; although in the Ag–Au alloys, the majority element segregates to the boundary. The width of the segregation profile is limited to approximately three to four (002) atomic planes. The classical theories for the segregation, and the effects of the relaxation with respect to either the atomic positions or the atomic concentrations, are discussed. The boundary thermodynamic properties depend sensitively on the magnitude of the boundary segregation, and some of them are shown to vary linearly with the magnitude of the grain boundary segregation.     

Enhanced Maturation of 3D Bioprinted Skeletal Muscle Tissue Constructs Encapsulating Soluble Factor-Releasing Microparticles

Several microfabrication technologies have been used to engineer native-like skeletal muscle tissues. However, the successful development of muscle remains a significant challenge in the tissue engineering field. Muscle tissue engineering aims to combine muscle precursor cells aligned within a highly organized 3D structure and biological factors crucial to support cell differentiation and maturation into functional myotubes and myofibers. In this study, the use of 3D bioprinting is proposed for the fabrication of muscle tissues using gelatin methacryloyl (GelMA) incorporating sustained insulin-like growth factor-1 (IGF-1)-releasing microparticles and myoblast cells. This study hypothesizes that functional and mature myotubes will be obtained more efficiently using a bioink that can release IGF-1 sustainably for in vitro muscle engineering. Synthesized microfluidic-assisted polymeric microparticles demonstrate successful adsorption of IGF-1 and sustained release of IGF-1 at physiological pH for at least 21 days. Incorporating the IGF-1-releasing microparticles in the GelMA bioink assisted in promoting the alignment of myoblasts and differentiation into myotubes. Furthermore, the myotubes show spontaneous contraction in the muscle constructs bioprinted with IGF-1-releasing bioink. The proposed bioprinting strategy aims to improve the development of new therapies applied to the regeneration and maturation of muscle tissues.