Experimental analysis of gene assembly with TopDown one-step real-time gene synthesis

Herein we present a simple, cost-effective TopDown (TD) gene synthesis method that eliminates the interference between the polymerase chain reactions (PCR) assembly and amplification in one-step gene synthesis. The method involves two key steps: (i) design of outer primers and assembly oligonucleotide set with a melting temperature difference of >10°C and (ii) utilization of annealing temperatures to selectively control the efficiencies of oligonucleotide assembly and full-length template amplification. In addition, we have combined the proposed method with real-time PCR to analyze the step-wise efficiency and the kinetics of the gene synthesis process. Gel electrophoresis results are compared with real-time fluorescence signals to investigate the effects of oligonucleotide concentration, outer primer concentration, stringency of annealing temperature, and number of PCR cycles. Analysis of the experimental results has led to insights into the gene synthesis process. We further discuss the conditions for preventing the formation of spurious DNA products. The TD real-time gene synthesis method provides a simple and efficient method for assembling fairly long DNA sequence, and aids in optimizing gene synthesis conditions. To our knowledge, this is the first report that utilizes real-time PCR for gene synthesis

Whole-body Dynamic Collision Avoidance with Time-varying Control Barrier Functions

Recently, there has been increasing attention in robot research towards the whole-body collision avoidance. In this paper, we propose a safety-critical controller that utilizes time-varying control barrier functions (time varying CBFs) constructed by Robo-centric Euclidean Signed Distance Field (RC-ESDF) to achieve dynamic collision avoidance. The RC-ESDF is constructed in the robot body frame and solely relies on the robot's shape, eliminating the need for real-time updates to save computational resources. Additionally, we design two control Lyapunov functions (CLFs) to ensure that the robot can reach its destination. To enable real-time application, our safety-critical controller which incorporates CLFs and CBFs as constraints is formulated as a quadratic program (QP) optimization problem. We conducted numerical simulations on two different dynamics of an L-shaped robot to verify the effectiveness of our proposed approach

Optimization-Based Motion Planning for Autonomous Parking Considering Dynamic Obstacle: A Hierarchical Framework

We present a hierarchical framework based on graph search and model predictive control (MPC) for electric autonomous vehicle (EAV) parking maneuvers in a tight environment. At high-level, only static obstacles are considered, and the scenario-based hybrid A* (SHA*), which is faster than the traditional hybrid A*, is designed to provide an initial guess (also known as a global path) for the parking task. To extract the velocity and acceleration profile from an initial guess, an optimal control problem (OCP) is built. At the low level, an NMPC-based strategy is used to avoid dynamic obstacles (also known as local planning). The efficacy of SHA* is evaluated through 148 different simulation schemes and the proposed hierarchical parking framework is demonstrated through a real-time parallel parking simulation

RORγ is a targetable master regulator of cholesterol biosynthesis in a cancer subtype.

Tumor subtype-specific metabolic reprogrammers could serve as targets of therapeutic intervention. Here we show that triple-negative breast cancer (TNBC) exhibits a hyper-activated cholesterol-biosynthesis program that is strongly linked to nuclear receptor RORγ, compared to estrogen receptor-positive breast cancer. Genetic and pharmacological inhibition of RORγ reduces tumor cholesterol content and synthesis rate while preserving host cholesterol homeostasis. We demonstrate that RORγ functions as an essential activator of the entire cholesterol-biosynthesis program, dominating SREBP2 via its binding to cholesterol-biosynthesis genes and its facilitation of the recruitment of SREBP2. RORγ inhibition disrupts its association with SREBP2 and reduces chromatin acetylation at cholesterol-biosynthesis gene loci. RORγ antagonists cause tumor regression in patient-derived xenografts and immune-intact models. Their combination with cholesterol-lowering statins elicits superior anti-tumor synergy selectively in TNBC. Together, our study uncovers a master regulator of the cholesterol-biosynthesis program and an attractive target for TNBC

TmPrime: fast, flexible oligonucleotide design software for gene synthesis

Herein we present TmPrime, a computer program to design oligonucleotide sets for gene assembly by both ligase chain reaction (LCR) and polymerase chain reaction (PCR). TmPrime offers much flexibility with no constraints on the gene and oligonucleotide lengths. The program divides the long input DNA sequence based on the input desired melting temperature, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences and potential formation of secondary structures. Our program also provides functions on sequence pooling to separate long genes into smaller pieces for multi-pool assembly and codon optimization for expression. The software has been successfully used in the design and synthesis of green fluorescent protein fragment (GFPuv) (760 bp), human protein kinase B-2 (PKB2) (1446 bp) and the promoter of human calcium-binding protein A4 (S100A4) (752 bp) using real-time PCR assembly with LCGreen I, which offers a novel approach to compare the efficiency of gene synthesis. The purity of assembled products is successfully estimated with the use of melting curve analysis, which would potentially eliminate the necessity for agarose gel electrophoresis. This program is freely available at http://prime.ibn.a-star.edu.sg

Self-perception evolution among university student TikTok users: evidence from China

The effects of short movies on social media platforms are gaining worldwide popularity and are now attracting global academic attention. Employing self-perception theory and qualitative research methodology, the study examines the influence of short video applications (TikTok) on app-user engagement and evaluates the self-perceived cognitive psychological understanding of Chinese university students. The findings show that identity, attitude change, emotional perception, and civic engagement are the most influential aspects of Chinese youths’ self-perceptions. Furthermore, the positive and negative correlated components influence the distribution of short video values. Such tactical use of personality construction contributes to the present psychological research of Chinese university students

The bracteatus pineapple genome and domestication of clonally propagated crops

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a 'one-step operation'. We sequenced the genome of Ananas comosus var. bracteatus CB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananas genomes. Cultivars 'Smooth Cayenne' and 'Queen' exhibited ancient and recent admixture, while 'Singapore Spanish' supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops

NTIRE 2023 Quality Assessment of Video Enhancement Challenge

This paper reports on the NTIRE 2023 Quality Assessment of Video Enhancement Challenge, which will be held in conjunction with the New Trends in Image Restoration and Enhancement Workshop (NTIRE) at CVPR 2023. This challenge is to address a major challenge in the field of video processing, namely, video quality assessment (VQA) for enhanced videos. The challenge uses the VQA Dataset for Perceptual Video Enhancement (VDPVE), which has a total of 1211 enhanced videos, including 600 videos with color, brightness, and contrast enhancements, 310 videos with deblurring, and 301 deshaked videos. The challenge has a total of 167 registered participants. 61 participating teams submitted their prediction results during the development phase, with a total of 3168 submissions. A total of 176 submissions were submitted by 37 participating teams during the final testing phase. Finally, 19 participating teams submitted their models and fact sheets, and detailed the methods they used. Some methods have achieved better results than baseline methods, and the winning methods have demonstrated superior prediction performance

Diagnosis of Interventional Transvaginal Maternal Diseases Based on Color Doppler Ultrasound

In recent years, with the development of color Doppler ultrasound technology in obstetrics, this noninvasive, direct, convenient, and sensitive inspection method has become one of the best methods to observe the fetal circulation in the uterus. This paper discusses the clinical value of using transvaginal color Doppler ultrasound in the differential diagnosis of ovarian corpus luteum disease and ectopic pregnancy disease. This paper selects 100 cases of ectopic pregnancy and 100 cases of pregnant corpus luteum as the experimental research objects. Clinical analysis of transvaginal color Doppler ultrasonography was performed on all patients. In the process of measuring the patient’s ectopic pregnancy, the size of the patient’s adnexal mass is mainly measured, and the blood flow spectrum is measured. The clinical choice of transvaginal color Doppler ultrasound method to distinguish ectopic pregnancy disease and corpus luteum pregnancy disease can play a significant value. It can be effectively diagnosed according to the type of disease, then effective methods can be studied for clinical treatment, the quality of life of patients with the two diseases can be significantly improved, and the clinical application value of color Doppler ultrasound can be improved

Perspectives on Using a Competitive Exclusion Approach to Control <i>Listeria monocytogenes</i> in Biological Soil Amendments of Animal Origin (BSAAO): A Review

Biological soil amendments of animal origin (BSAAO), such as animal waste or animal-waste-based composts, may contain foodborne pathogens such as Listeria monocytogenes. Due to the ubiquitous nature of Listeria, it is essential to understand the behavior of L. monocytogenes in BSAAO in order to develop preharvest prevention strategies to reduce pathogen contamination. As biological control agents, competitive exclusion (CE) microorganisms have been widely utilized in agriculture to control plant- or foodborne pathogens. Due to the diverse microbial community, animal wastes and composts are the potential sources for isolating CE strains for pathogen control. To explore the potential of using CE to control L. monocytogenes in BSAAO, we thoroughly reviewed the studies on the fate of L. monocytogenes in the agriculture field, and in the isolation and identification of CE from different matrices, and the applications of CE as a biological control method. Future studies using a next-generation sequencing approach to identify and characterize CE strains in complex microbial communities can provide a comprehensive picture of the microbial interactions between invading pathogens and the indigenous microbiota in BSAAO. This comprehensive review will provide insight into the development of effective biological control measures for preventing L. monocytogenes contamination in the agricultural field and enhancing food safety