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Abstract The interphase genome is dynamically organized in the nucleus and decorated with chromatin-associated RNA (caRNA). It remains unclear whether the genome architecture modulates the spatial distribution of caRNA and vice versa. Here, we generate a resource of genome-wide RNA-DNA and DNA-DNA contact maps in human cells. These maps reveal the chromosomal domains demarcated by locally transcribed RNA, hereafter termed RNA-defined chromosomal domains. Further, the spreading of caRNA is constrained by the boundaries of topologically associating domains (TADs), demonstrating the role of the 3D genome structure in modulating the spatial distribution of RNA. Conversely, stopping transcription or acute depletion of RNA induces thousands of chromatin loops genome-wide. Activation or suppression of the transcription of specific genes suppresses or creates chromatin loops straddling these genes. Deletion of a specific caRNA-producing genomic sequence promotes chromatin loops that straddle the interchromosomal target sequences of this caRNA. These data suggest a feedback loop where the 3D genome modulates the spatial distribution of RNA, which in turn affects the dynamic 3D genome organization.

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, thus termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA–promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial–nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.

Gluconobacter oxydans is an important Gram-negative industrial microorganism that produces vitamin C and other products due to its efficient membrane-bound dehydrogenase system. Its incomplete oxidation system has many crucial industrial applications. However, it also leads to slow growth and low biomass, requiring further metabolic modification for balancing the cell growth and incomplete oxidation process. As a non-model strain, G. oxydans lacks efficient genome editing tools and cannot perform rapid multi-gene editing and complex metabolic network regulation. In the last 15 years, our laboratory attempted to deploy multiple CRISPR/Cas systems in different G. oxydans strains and found none of them as functional. In this study, Cpf1-based or dCpf1-based CRISPRi was constructed to explore the targeted binding ability of Cpf1, while Cpf1–FokI was deployed to study its nuclease activity. A study on Cpf1 found that the CRISPR/Cpf1 system could locate the target genes in G. oxydans but lacked the nuclease cleavage activity. Therefore, the CRISPR/Cpf1–FokI system based on FokI nuclease was constructed. Single-gene knockout with efficiency up to 100% and double-gene iterative editing were achieved in G. oxydans. Using this system, AcrVA6, the anti-CRISPR protein of G. oxydans was discovered for the first time, and efficient genome editing was realized.

The effects of biogas residue as a substrate on ginseng growth and its feasibility for ginseng cultivation are unclear. The present study used biogas residue at different concentrations and maturity levels to cultivate ginseng. The biological characteristics of ginseng, soil physiochemical indices, and ginseng and soil microbial communities were investigated. The results showed that with increasing ginseng content and maturity, the total fresh weight, total length and saponin content significantly increased. The enzyme activities of soil, NO3--N, and available phosphorus also increased. The microbiome analysis revealed that with the addition of biogas residue, microorganisms related to plant growth promotion, such as Chloroflexi, Gemmatimonadota and Mortierellomycota, were more common in the plant or rhizosphere soil. The results based on the co-occurrence network showed that the structure of the bacterial community was more stable than that of the fungal community with increasing biogas residue content. Our results indicated that biogas residue could be used as a ginseng cultivation substrate and promote growth.

l-Tyrosine, an aromatic non-essential amino acid, is the raw material for many important chemical products, including levodopa, resveratrol, and hydroxytyrosol. It is widely used in the food, drug, and chemical industries. There are many studies on the synthesis of l-tyrosine by microorganisms, however, the low titer of l-tyrosine limited the industrial large-scale production. In order to enhance l-tyrosine production in Escherichia coli, the expression of key enzymes in the shikimate pathway was up- or down-regulated. The l-tyrosine transport system and the acetic acid biosynthesis pathway were modified to further enhance l-tyrosine production. In addition, the phosphoketolase pathway was introduced in combination with cofactor engineering to redirect carbon flux to the shikimate pathway. Finally, after adaptive laboratory evolution to low pH an optimal strain was obtained. The strain can produce 92.5 g/L of l-tyrosine in a 5-L fermenter in 62 h, with a yield of 0.266 g/g glucose.

The article focuses on centrifugal pumps are essential mechanical components for liquid delivery in many biomedical systems whose miniaturization can promote innovative disease treatment approaches. It mentions soft materials and flexible electronics to achieve soft magnetic levitation micropumps (SMLMs) and rotation speed of per min to pump liquids with various viscosities. It also mentions development of SMLMs not only demonstrates the possibility to replace rigid rotating structures.

Abstract L‐Sorbosone dehydrogenase (SNDH) is a key enzyme involved in the biosynthesis of 2‐keto‐L‐gulonic acid , which is a direct precursor for the industrial scale production of vitamin C. Elucidating the structure and the catalytic mechanism is essential for improving SNDH performance. By solving the crystal structures of SNDH from Gluconobacter oxydans WSH‐004, a reversible disulfide bond between Cys295 and the catalytic Cys296 residues is discovered. It allowed SNDH to switch between oxidation and reduction states, resulting in opening or closing the substrate pocket. Moreover, the Cys296 is found to affect the NADP+ binding pose with SNDH. Combining the in vitro biochemical and site‐directed mutagenesis studies, the redox‐based dynamic regulation and the catalytic mechanisms of SNDH are proposed. Moreover, the mutants with enhanced activity are obtained by extending substrate channels. This study not only elucidates the physiological control mechanism of the dehydrogenase, but also provides a theoretical basis for engineering similar enzymes.

BackgroundMild cognitive impairment (MCI) is a critical stage of dementia. Previous reviews have suggested that physical exercise combined with non-invasive brain stimulation is more beneficial for improving cognitive function. However, no targeted studies have confirmed the effect of Tai Chi combined with transcranial direct current stimulation (tDCS) on the improvement of cognitive function in patients with MCI. Thus, this randomized trial was conducted to assess the effect of Tai Chi combined with tDCS on the cognitive performance of patients with MCI.MethodsFrom April 2018 to February 2020, a randomized, single-blind clinical trial was conducted, involving 180 participants with MCI who were divided into four intervention groups: Tai Chi combined with tDCS (TCT), Tai Chi combined with sham tDCS (TCS), walking combined with tDCS (WAT), and walking combined with sham tDCS (WAS). All participants were assessed at baseline and 12 weeks for global cognitive function, memory, attention, and executive function.ResultsAt baseline, there were no significant differences in age, gender, education duration, body mass index, or the Baker Depression Inventory among the four groups (P ≥ 0.05). After 12 weeks of intervention, the TCT group showed greater improvements in MOCA scores, memory quotient scores, and digit-symbol coding task reaction time compared to the TCS, WAS, and WAT groups (P < 0.05). The TCT group also had a shorter Stroop test color reaction time compared to the WAS and WAT groups (P < 0.05), a higher increase in Auditory Verbal Learning Test-immediate recall than the TCS and WAT groups (P < 0.05), a shorter visual reaction time than the TCS group (P < 0.05), and a shorter sustained attention time compared to the WAT group (P < 0.05).ConclusionTai Chi combined with tDCS effectively improves global cognitive performance, memory, execution function, and attention in patients with MCI. These findings suggest the potential clinical use of Tai Chi combined with tDCS as a physical exercise combined with a non-invasive brain stimulation intervention to improve cognitive function in older adults with MCI.Clinical trial registrationChiCTR1800015629.

Abstract Cereals are the main food for mankind. The grain shape extraction and filled/unfilled grain recognition are meaningful for crop breeding and genetic analysis. The conventional measuring method is mainly manual, which is inefficient, labor-intensive and subjective. Therefore, a novel method was proposed to extract the phenotypic traits of cereal grains based on point clouds. First, a structured light scanner was used to obtain the grains point cloud data. Then, the single grain segmentation was accomplished by image preprocessing, plane fitting, region growth clustering. The length, width, thickness, surface area and volume was calculated by the specified analysis algorithms for grain point cloud. To demonstrate this method, experimental materials included rice, wheat and corn were tested. Compared with manual measurement results, the average measurement error of grain length, width and thickness was 2.07%, 0.97%, 1.13%, and the average measurement efficiency was about 9.6 s per grain. In addition, the grain identification model was conducted with 25 grain phenotypic traits, using 6 machine learning methods. The results showed that the best accuracy for filled/unfilled grain classification was 90.184%.The best accuracy for indica and japonica identification was 99.950%, while for different varieties identification was only 47.252%. Therefore, this method was proved to be an efficient and effective way for crop research.

Plant-associated microbes play important roles in plant health and disease. Mortierella is often found in the plant rhizosphere, and its possible functions are not well known, especially in medical plants. Mortierella alpina isolated from ginseng soil was used to investigate its effects on plant disease. The promoting properties and interactions with rhizospheric microorganisms were investigated in a medium. Further, a pot experiment was conducted to explore its effects on ginseng root rot disease. Physicochemical properties, high-throughput sequencing, network co-occurrence, distance-based redundancy analysis (db-RDA), and correlation analysis were used to evaluate their effects on the root rot pathogen. The results showed that Mortierella alpina YW25 had a high indoleacetic acid production capacity, and the maximum yield was 141.37 mg/L at 4 days. The growth of M. alpina YW25 was inhibited by some probiotics (Bacillus, Streptomyces, Brevibacterium, Trichoderma, etc.) and potential pathogens (Cladosporium, Aspergillus, etc.), but it did not show sensitivity to the soil-borne pathogen Fusarium oxysporum. Pot experiments showed that M. alpina could significantly alleviate the diseases caused by F. oxysporum, and increased the available nitrogen and phosphorus content in rhizosphere soil. In addition, it enhanced the activities of soil sucrase and acid phosphatase. High-throughput results showed that the inoculation of M. alpina with F. oxysporum changed the microbial community structure of ginseng, stimulated the plant to recruit more plant growth-promoting bacteria, and constructed a more stable microbial network of ginseng root. In this study, we found and proved the potential of M. alpina as a biocontrol agent against F. oxysporum, providing a new idea for controlling soil-borne diseases of ginseng by regulating rhizosphere microorganisms.

The wheat grain three-dimensional (3D) phenotypic characters are of great significance for final yield and variety breeding, and the ventral sulcus traits are the important factors to the wheat flour yield. The wheat grain trait measurements are necessary; however, the traditional measurement method is still manual, which is inefficient, subjective, and labor intensive; moreover, the ventral sulcus traits can only be obtained by destructive measurement. In this paper, an intelligent analysis method based on the structured light imaging has been proposed to extract the 3D wheat grain phenotypes and ventral sulcus traits. First, the 3D point cloud data of wheat grain were obtained by the structured light scanner, and then, the specified point cloud processing algorithms including single grain segmentation and ventral sulcus location have been designed; finally, 28 wheat grain 3D phenotypic characters and 4 ventral sulcus traits have been extracted. To evaluate the best experimental conditions, three-level orthogonal experiments, which include rotation angle, scanning angle, and stage color factors, were carried out on 125 grains of 5 wheat varieties, and the results demonstrated that optimum conditions of rotation angle, scanning angle, and stage color were 30°, 37°, black color individually. Additionally, the results also proved that the mean absolute percentage errors (MAPEs) of wheat grain length, width, thickness, and ventral sulcus depth were 1.83, 1.86, 2.19, and 4.81%. Moreover, the 500 wheat grains of five varieties were used to construct and validate the wheat grain weight model by 32 phenotypic traits, and the cross-validation results showed that the R2 of the models ranged from 0.77 to 0.83. Finally, the wheat grain phenotype extraction and grain weight prediction were integrated into the specialized software. Therefore, this method was demonstrated to be an efficient and effective way for wheat breeding research.

Abstract Background To prevent and control dementia, many scholars have focused on the transition stage between normal ageing and dementia, mild cognitive impairment (MCI) which is a key interventional target for dementia. Studies have shown that non-invasive brain stimulation (NIBS) is beneficial to improve cognitive function of MCI patients. However, whether NIBS is conducive to the protection of cognitive ability in MCI patients remains unknown due to limited evidence. The aim of the study was to systematically evaluate the modulation effect of NIBS on cognitive function (global cognitive ability and specific domains of cognition) in patients with MCI. Results A total of 11 RCTs comprising a total of 367 MCI participants. Meta-analysis showed that NIBS can significantly improve global cognition (n = 271, SMD = 0.94, 95% CI 0.47–1.41, p

Aiming at the problem of apple branch obstacle localization in fruit picking process of harvesting robot manipulator, in order to obtain three-dimensional information of the apple branch obstacle, the binocular stereo vision localization method of apple branch obstacle is proposed. Firstly, branch skeleton is extracted by morphological thinning method and then the feature skeleton is obtained after removing the false branch and recovering the occluded branch. After that, the endpoints and bifurcation points regarded as match feature points are extracted from skeleton, and the stereo matching algorithm based on features is adopted. Then, the depth information of branch obstacle is obtained on the basis of triangulation theory. Finally, the experiment results for apple tree branches localization show that the error lies in ±6.2 mm. Moreover, the error is merely ±1.5 mm when the distance between the object and the binocular camera is 1000 mm, which meets with localization accuracy requirements of apple harvesting robot visual system.

The effect of different atomic substitutions at Mn sites on the magnetic and magnetocaloric properties in Ni50Mn35Co2Sn13 alloy has been studied in detail. The substitution of Ni or Co for Mn atoms might lower the Mn content at Sn sites, which would reduce the d-d hybridization between Ni 3d eg states and the 3d states of excess Mn atoms at Sn sites, thus leading to the decrease of martensitic transformation temperature TM in Ni51Mn34Co2Sn13 and Ni50Mn34Co3Sn13 alloys. On the other hand, the substitution of Sn for Mn atoms in Ni50Mn34Co2Sn14 would enhance the p-d covalent hybridization between the main group element (Sn) and the transition metal element (Mn or Ni) due to the increase of Sn content, thus also reducing the TM by stabilizing the parent phase. Due to the reduction of TM, a magnetostructural martensitic transition from FM austenite to weak-magnetic martensite is realized in Ni51Mn34Co2Sn13 and Ni50Mn34Co2Sn14, resulting in a large magnetocaloric effect around room temperature. For a low field change of 3 T, the maximum ∆SM reaches as high as 30.9 J/kg K for Ni50Mn34Co2Sn14. A linear dependence of ΔSM upon μ0H has been found in Ni50Mn34Co2Sn14, and the origin of this linear relationship has been discussed by numerical analysis of Maxwell’s relation.

In this paper we introduce OpenEnsembles, a Python toolkit for performing and analyzing ensemble clustering. Ensemble clustering is the process of creating many clustering solutions for a given dataset and utilizing the relationships observed across the ensemble to identify final solutions, which are more robust, stable or better than the individual solutions within the ensemble. The OpenEnsembles library provides a unified interface for applying transformations to data, clustering data, visualizing individual clustering solutions, visualizing and finishing the ensemble, and calculating validation metrics for a clustering solution for any given partitioning of the data. We have documented examples of using OpenEnsembles to create, analyze, and visualize a number of different types of ensemble approaches on toy and example datasets. OpenEnsembles is released under the GNU General Public License version 3, can be installed via Conda or the Python Package Index (pip), and is available at https://github.com/NaegleLab/OpenEnsembles. [ABSTRACT FROM AUTHOR]