A KDELR-mediated ER-retrieval system modulates mitochondrial functions via the unfolded protein response in fission yeast.

KDELR (Erd2 [ER retention defective 2] in yeasts) is a receptor protein that retrieves endoplasmic reticulum (ER)-resident proteins from the Golgi apparatus. However, the role of the KDELR-mediated ER-retrieval system in regulating cellular homeostasis remains elusive. Here, we show that the absence of Erd2 triggers the unfolded protein response (UPR) and enhances mitochondrial respiration and reactive oxygen species in an UPR-dependent manner in the fission yeast Schizosaccharomyces pombe. Moreover, we perform transcriptomic analysis and find that the expression of genes related to mitochondrial respiration and the tricarboxylic acid cycle is upregulated in a UPR-dependent manner in cells lacking Erd2. The increased mitochondrial respiration and reactive oxygen species production is required for cell survival in the absence of Erd2. Therefore, our findings reveal a novel role of the KDELR-Erd2-mediated ER-retrieval system in modulating mitochondrial functions and highlight its importance for cellular homeostasis in the fission yeast.

Application of extremophile cell factories in industrial biotechnology.

Due to the extreme living conditions, extremophiles have unique characteristics in morphology, structure, physiology, biochemistry, molecular evolution mechanism and so on. Extremophiles have superior growth and synthesis capabilities under harsh conditions compared to conventional microorganisms, allowing for unsterilized fermentation processes and thus better performance in low-cost production. In recent years, due to the development and optimization of molecular biology, synthetic biology and fermentation technology, the identification and screening technology of extremophiles has been greatly improved. In this review, we summarize techniques for the identification and screening of extremophiles and review their applications in industrial biotechnology in recent years. In addition, the facts and perspectives gathered in this review suggest that next-generation industrial biotechnology (NGIBs) based on engineered extremophiles holds the promise of simplifying biofuturing processes, establishing open, non-sterilized continuous fermentation production systems, and utilizing low-cost substrates to make NGIBs attractive and cost-effective bioprocessing technologies for sustainable manufacturing.

Influential Signs of Dry Eye-Related Ocular Symptoms in Participants With Unstable Tear Film.

PURPOSE: The aim of this study was to investigate the factors influencing dry eye disease (DED)-related ocular symptoms in participants with short fluorescein tear break-up time (FTBUT). METHODS: This cross-sectional study included 82 participants with short FTBUT (<10 seconds). Examinations included Ocular Surface Disease Index (OSDI), FTBUT, average noninvasive tear break-up time (NIBUTave), lid wiper epitheliopathy, lipid layer thickness, blink rate, partial blink, tear meniscus height, and meibomian gland (MG) evaluation which included ratio of residual MG area (RMGA) and MG grade in tarsal plates. One-way analysis of variance was used to detect differences between symptomatic tear film instability group (FTBUT <5 s, OSDI ≥13), asymptomatic tear film instability group (FTBUT <5 s, OSDI <13), and control group (FTBUT ≥5 s, OSDI <13). A bivariate correlation, partial correlation, and multiple linear regression analyses were used to identify major factors. Only the right eye was included. RESULTS: Among the participants with FTBUT <5 seconds, symptomatic group showed less upper RMGA ( P < 0.001) and NIBUTave ( P = 0.010). OSDI was negatively associated with upper RMGA ( r = -0.450, P < 0.001) and NIBUTave ( r = -0.414, P = 0.001), and positively associated with upper MG grade ( r = 0.277, P = 0.027). Linear regression analysis showed that the upper RMGA significantly affected OSDI (B = -41.895, P = 0.001), while not significantly correlated with age, upper MG grade, and NIBUTave. CONCLUSIONS: The upper RMGA might be the main factor affecting DED-related discomfort in participants with unstable tear film, indicating an early ocular change in DED.

Three Hertz postural leg tremor impairs posture maintenance in multiple system atrophy-cerebellar type.

BACKGROUND: Three-Hz postural leg tremor has recently been identified as highly prevalent in patients with the cerebellar type of multiple system atrophy, but its impact on posture maintenance remains poorly understood. PATIENTS AND METHODS: Thirty-seven patients with spinocerebellar ataxia and 58 others with cerebellar type of multiple system atrophy were given Synapsys posturography examinations. Fifty-three healthy controls were also tested. Low, medium, and high-frequency sway were recorded to compute energy values. Frequency shift and postural strategy predominance were evaluated from the postural sway distributions, mainly from the proportions of higher frequency values among the total values. The trajectories of postural sway components were evaluated with the generalized additive mixed model. Distributions of the components and their relationships with falls and tremors were assessed through repeated measures correlation analysis. RESULTS: As the test difficulty increased, the standard controls showed slight increases in the energy values at every frequency. Distributions of the higher frequency (>0.5 Hz) values increased escalatingly with test difficulty, illustrating frequency shifts and hip strategy predominance. Medium and high-frequency values were strongly and positively inter-correlated in normal stances, but this was not observed among the spinocerebellar ataxia or multiple system atrophy patients. Unlike normal stances, the proportion of medium frequency values was negatively related to the total value among the spinocerebellar ataxia and multiple system atrophy patients, implying a failure of frequency shift in response to perturbation. Medium frequency proportions were also inversely correlated with tremors among the multiple system atrophy patients. CONCLUSIONS: The observed synchronized changes in medium and high-frequency postural sway indicate that they constitute a complete hip strategy for posture control. The strategy was rigid in those with spinocerebellar ataxia but completely disrupted in those with multiple system atrophy. Three Hertz postural leg tremors destabilize the ankle joints and interfere with postural adjustment among those with multiple system atrophy.

The Green Synthesis of Reduced Graphene Oxide Using Ellagic Acid: Improving the Contrast-Enhancing Effect of Microbubbles in Ultrasound.

There is an urgent need to realize precise clinical ultrasound with ultrasound contrast agents that provide high echo intensity and mechanical index tolerance. Graphene derivatives possess exceptional characteristics, exhibiting great potential in fabricating ideal ultrasound contrast agents. Herein, we reported a facile and green approach to synthesizing reduced graphene oxide with ellagic acid (rGO-EA). To investigate the application of a graphene derivative in ultrasound contrast agents, rGO-EA was dispersed in saline solution and mixed with SonoVue (SV) to fabricate SV@rGO-EA microbubbles. To determine the properties of the product, analyses were performed, including ultraviolet-visible spectroscopy (UV-vis), Fourier-transform infrared spectroscopy (FTIR), Raman spectroscopy, transmission electron microscopy (TEM), thermal gravimetric analysis (TGA), X-ray photoelectron spectrum (XPS), X-ray diffraction analysis (XRD) and zeta potential analysis. Additionally, cell viability measurements and a hemolysis assay were conducted for a biosafety evaluation. SV@rGO-EA microbubbles were scanned at various mechanical index values to obtain the B-mode and contrast-enhanced ultrasound (CEUS) mode images in vitro. SV@rGO-EA microbubbles were administered to SD rats, and their livers and kidneys were imaged in CEUS and B-mode. The absorption of rGO-EA resulted in an enhanced echo intensity and mechanical index tolerance of SV@rGO-EA, surpassing the performance of SV microbubbles both in vitro and in vivo. This work exhibited the application potential of graphene derivatives in the field of ultrasound precision medicine.

Bacillus sp. as a microbial cell factory: Advancements and future prospects.

Bacillus sp. is one of the most distinctive gram-positive bacteria, able to grow efficiently using cheap carbon sources and secrete a variety of useful substances, which are widely used in food, pharmaceutical, agricultural and environmental industries. At the same time, Bacillus sp. is also recognized as a safe genus with a relatively clear genetic background, which is conducive to the industrial production of target metabolites. In this review, we discuss the reasons why Bacillus sp. has been so extensively studied and summarize its advances in systems and synthetic biology, engineering strategies to improve microbial cell properties, and industrial applications in several metabolic engineering applications. Finally, we present the current challenges and possible solutions to provide a reliable basis for Bacillus sp. as a microbial cell factory.

Sound transmission across locally resonant honeycomb sandwich meta-structures with large spatial periodicity.

Honeycomb sandwich structures have been widely used in the field of engineering owing to their outstanding mechanical properties. However, for a honeycomb sandwich structure with large spatial periodicity, there is a low-frequency sound insulation valley. Here, the sound transmission across locally resonant honeycomb sandwich meta-structures was investigated to overcome this sound-insulation valley. An analytical model was developed based on the space-harmonic approach and the low-frequency sound insulation valley was determined analytically and numerically. The results indicate that the resonator distributed at the center of the face panel has a significant impact on the sound transmission performance of the honeycomb sandwich structure, whereas the resonator distributed on the wall of the honeycomb core does not contribute to overcoming this sound-insulation valley. Based on the research results, a design strategy for overcoming this sound-insulation valley was determined by tuning the damping parameter and constructing graded resonators. Moreover, sound transmission under the excitation of oblique incidence sound waves was also investigated. Compared with the method of filling porous materials, the proposed design method is more effective, and more importantly, the mass of the resonator is only 1.23% of that of the porous materials.

DSEMR: A database for special environment microorganisms resource and associating them with synthetic biological parts.

Special environmental microorganisms are considered to be of great industrial application value because of their special genotypes, physiological functions and metabolites. The research and development of special environmental microorganisms will certainly bring about some innovations in biotechnology processes and change the face of bioengineering. The Special Environmental Microbial Database (DSEMR) is a comprehensive database that provides information on special environmental microbial resources and correlates them with synthetic biological parts. DSEMR aggregates information on specific environmental microbial genomes, physiological properties, culture media, biological parts, and metabolic pathways, and provides online tool analysis data, including 5268 strains from 620 genera, 31 media, and 42,126 biological parts. In short, DSEMR will become an important resource for the study of microorganisms in special environments and actively promote the development of synthetic biology.

Enzymolysis-based RNA pull-down identifies YTHDC2 as an inhibitor of antiviral innate response.

The innate immune response must be terminated in a timely manner at the late stage of infection to prevent unwanted inflammation. The role of m6A-modified RNAs and their binding partners in this process is not well known. Here, we develop an enzymolysis-based RNA pull-down (eRP) method that utilizes the immunoglobulin G-degrading enzyme of Streptococcus pyogenes (IdeS) to fish out m6A-modified RNA-associated proteins. We apply eRP to capture the methylated single-stranded RNA (ssRNA) probe-associated proteins and identify YT521-B homology domain-containing 2 (YTHDC2) as the m6A-modified interferon ß (IFN-ß) mRNA-binding protein. YTHDC2, induced in macrophages at the late stage of virus infection, recruits IFN-stimulated exonuclease ISG20 (IFN-stimulated exonuclease gene 20) to degrade IFN-ß mRNA, consequently inhibiting antiviral innate immune response. In vitro and in vivo deficiency of YTHDC2 increases IFN-ß production at the late stage of viral infection. Our findings establish an eRP method to effectively identify RNA-protein interactions and add mechanistic insight to the termination of innate response for maintaining homeostasis.

Case Report: Clinical application of immunotherapy-based combination regimen in primary osteosarcoma of the uterus.

Primary osteosarcoma of the uterus is an extremely rare pure heterologous sarcoma of the uterus. The relevant available information is limited to case reports. To date, only 31 cases of this type of cancer have been reported. Here, we report the first clinical experience with the administration of an immunotherapy-based combination regimen for multiple metastatic primary osteosarcomas of the uterus. The patient had undergone multiple treatments prior to this regimen, but her condition continued to progress. However, after 3 cycles of immunotherapy combined with targeted therapy and chemotherapy, a review showed that the disease was stable and even in partial remission. The patient has a good quality of life, and long-term survival is expected.

Rapid construction of Escherichia coli chassis with genome multi-position integration of isopentenol utilization pathway for efficient and stable terpenoid accumulation.

The isopentenol utilization pathway (IUP) is potential in terpenoids synthesis. This study aimed to construct IUP-employed Escherichia coli chassis for stably synthesizing terpenoids. As to effectiveness, promotor engineering strategy was employed to regulate IUP expression level, while ribosome-binding site (RBS) library of the key enzyme was constructed for screening the optimal RBS, followed by optimization of concentration of inducer and substrates, the titer of reporting production, lycopene, from 0.087 to 8.67 mg OD600 -1 . As about stability, the IUP expression cassette was integrated into the genome through transposition tool based on CRISPR-associated transposases. Results showed that the strain with 13 copies produced 1.78-fold lycopene titer that of the controlled strain with IUP-harbored plasmid, and it exhibited stable expression after ten successions while the plasmid loss was observed in the controlled strain in the 3rd succession. This strategy provides valuable information for rapid construction of highly effective and stable chassis employing IUP for terpenoids production.

Air quality policy should quantify effects on disparities.

New tools can guide US policies to better target and reduce racial and socioeconomic disparities in air pollution exposure.

Pathogenicity characterization of PRRSV-1 181187-2 isolated in China.

PRRSV-1 has caused more clinical infections in pigs in Chinese swine herds in recent years, however, the pathogenicity of PRRSV-1 in China is unclear. In order to study the pathogenicity of PRRSV-1, in this study, a PRRSV-1 strain, 181187-2, was isolated in primary alveolar macrophage (PAM) cells from a farm where abortions had been reported in China. The complete genome of 181187-2 was 14932 bp excluding Poly A, with 54-amino acid continuous deletion in the Nsp2 gene and 1 amino deletion in ORF3 gene compared with LV. Additionally, the piglets inoculated with strain 181187-2 by intranasal and intranasal plus intramuscular injection, animal experiments showed clinical symptoms including transient fever and depression, with no death. The obvious histopathological lesions including interstitial pneumonia and lymph node hemorrhage, and there were no significant differences in clinical symptoms and histopathological lesions with different challenge ways. Our results indicated that PRRSV -1 181187-2 was a moderately pathogenic strain in piglets.

Ginsenoside Rg1 ameliorates Alzheimer's disease pathology via restoring mitophagy.

Background: Alzheimer's disease (AD) is a common form of dementia, and impaired mitophagy is a hallmark of AD. Mitophagy is mitochondrial-specific autophagy. Ginsenosides from Ginseng involve in autophagy in cancer. Ginsenoside Rg1 (Rg1 hereafter), a single compound of Ginseng, has neuroprotective effects on AD. However, few studies have reported whether Rg1 can ameliorate AD pathology by regulating mitophagy. Methods: Human SH-SY5Y cell and a 5XFAD mouse model were used to investigate the effects of Rg1. Rg1 (1µM) was added to ß-amyloid oligomer (AßO)-induced or APPswe-overexpressed cell models for 24 hours. 5XFAD mouse models were intraperitoneally injected with Rg1 (10 mg/kg/d) for 30 days. Expression levels of mitophagy-related markers were analyzed by western blot and immunofluorescent staining. Cognitive function was assessed by Morris water maze. Mitophagic events were observed using transmission electron microscopy, western blot, and immunofluorescent staining from mouse hippocampus. The activation of the PINK1/Parkin pathway was examined using an immunoprecipitation assay. Results: Rg1 could restore mitophagy and ameliorate memory deficits in the AD cellular and/or mouse model through the PINK1-Parkin pathway. Moreover, Rg1 might induce microglial phagocytosis to reduce ß-amyloid (Aß) deposits in the hippocampus of AD mice. Conclusion: Our studies demonstrate the neuroprotective mechanism of ginsenoside Rg1 in AD models. Rg1 induces PINK-Parkin mediated mitophagy and ameliorates memory deficits in 5XFAD mouse models.

Improving acetoin production through construction of a genome-scale metabolic model.

Acetoin was widely used in food, medicine, and other industries, because of its unique fragrance. Bacillus amyloliquefaciens was recognized as a safe strain and a promising acetoin producer in fermentation. However, due to the complexity of its metabolic network, it had not been fully utilized. Therefore, a genome-scale metabolic network model (iJYQ746) of B. amyloliquefaciens was constructed in this study, containing 746 genes, 1736 reactions, and 1611 metabolites. The results showed that Mg2+, Mn2+, and Fe2+ have inhibitory effects on acetoin. When the stirring speed was 400 rpm, the maximum titer was 49.8 g L-1. Minimization of metabolic adjustments (MOMA) was used to identify potential metabolic modification targets 2-oxoglutarate aminotransferase (serC, EC 2.6.1.52) and glucose-6-phosphate isomerase (pgi, EC 5.3.1.9). These targets could effectively accumulate acetoin by increasing pyruvate content, and the acetoin synthesis rate was increased by 610% and 10%, respectively. This provides a theoretical basis for metabolic engineering to reasonably transform B. amyloliquefaciens and produce acetoin.

Metabolic analysis of Schizochytrium sp. mutants with high EPA content achieved with ARTP mutagenesis screening.

Eicosapentaenoic acid (EPA) belonged to the ω-3 series of polyunsaturated fatty acids and had physiological functions lipid as regulating blood lipid and preventing cardiovascular diseases. Schizochytrium sp. was considered to be a potential industrial fermentation strain of EPA because of its fast growth, high oil content, and simple fatty acid composition. However, Schizochytrium sp. produced EPA with low production efficiency and a long synthesis path. This research aims to improve the yield of EPA in Schizochytrium sp. by ARTP mutagenesis and to reveal the mechanism of high-yield EPA through transcriptome analysis. ARTP mutagenesis screening yielded the mutant M12 that whereas the productivity of EPA increased 108% reaching 0.48 g/L, the total fatty acid concentration was 13.82 g/L with an increase of 13.7%. The transcriptomics revealed 2995 differentially expressed genes were identified between M12 and the wild-type strain and transcripts involved in carbohydrate, amino acid, energy, and lipid metabolism were up-regulated. Among them, the hexokinase (HK) and the phosphofructokinase genes (PFK), which can catalyze pyruvate to acetyl-CoA, were increased 2.23-fold and 1.78-fold. Glucose-6-phosphate dehydrogenase (G6PD) and glutamate dehydrogenase (GLDH), which can both generate NADPH, were increased by 1.67-fold and 3.11-fold. Furthermore, in the EPA synthesis module, the expression of 3-oxoacyl-[acyl-carrier protein] reductase(fabG) and carbonyl reductase 4 / 3-oxoacyl-[acyl-carrier protein] reductase beta subunit(CBR4), also up-regulated 1.11-fold and 2.67-fold. These may lead to increases in cell growth. The results provide an important reference for further research on promoting fatty acid and EPA accumulation in Schizochytrium sp.

In Situ STING-Activating Nanovaccination with TIGIT Blockade for Enhanced Immunotherapy of Anti-PD-1-Resistant Tumors.

Immunotherapies comprising programmed cell death protein 1/PD ligand 1 (PD-1/PD-L1) immune checkpoint inhibitors are effective cancer treatments. However, the low response rate and immunoresistance resulting from alternative immune checkpoint upregulation and inefficient immune stimulation by T cells are problematic. The present report describes a biomimetic nanoplatform that simultaneously blocks the alternative T-cell immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domain (TIGIT) checkpoint and activates the stimulator of interferon genes (STING) signaling pathway in situ for enhanced antitumor immunity. The nanoplatform is engineered by fusing a red blood cell membrane with glutathione-responsive liposome-encapsulated cascade-activating chemoagents (ß-lapachone and tirapazamine), and anchoring them with a detachable TIGIT block peptide (named as RTLT). In the tumor environment, the peptide is spatiotemporally released to reverse T-cell exhaustion and restore antitumor immunity. The cascade activation of chemotherapeutic agents causes DNA damage and inhibits the repair of double-stranded DNA, which induces robust in situ STING activation for an efficient immune response. The RTLT inhibits anti-PD-1-resistant tumor growth, and prevents tumor metastasis and recurrence in vivo by inducing antigen-specific immune memory. This biomimetic nanoplatform thus provides a promising strategy for in situ cancer vaccination.

Landslide susceptibility prediction considering land use change and human activity: A case study under rapid urban expansion and afforestation in China.

China has been subject to rapid urban expansion and afforestation since the economic reform in 1978. However, the influence of land use and cover changes (LUCCs) and human activities on landslide occurrence is often ignored in landslide susceptibility mapping and zonation (LSMZ). In this study, Enshi City, China, was selected as the study area because of dramatic LUCCs during the last two decades. This study divided landslide affecting factors (AFs) into base affecting factors (BAFs) and land-related affecting factors (LAFs), and 15 landslide susceptibility maps were created by three different types of models. The results showed that the combination 6 of heuristic multi-layer perceptron model with LAFs (HMLP-LAFC6) model obtained the highest model performance. In addition, any factor combinations of HMLP-LAF model outperformed other two types of models, and the use of land use and cover (LULC) in different periods as well as LUCCs may significantly impact the model performance. Given that land policy adjustments are normally core drivers of LUCC in China, a land planning based LSMZ framework was proposed, which is suitable for LSMZ in rapid LUCC regions with radical land policies. Finally, this paper strongly suggests developing more hybrid models that coupling dynamic AFs, clarifying the quantitative boundaries of time-irrelevant and dynamic AFs, increasing the accuracy of LULC prediction, and improving the abilities of bilateral understanding for effective, integrated, and systematic management of land planning and landslide hazards.

Decoding transcriptional regulation via a human gene expression predictor.

Transcription factors (TFs) regulate cellular activities by controlling gene expression, but a predictive model describing how TFs quantitatively modulate human transcriptomes is lacking. We construct a universal human gene expression predictor named EXPLICIT-Human and utilize it to decode transcriptional regulation. Using the expression of 1613 TFs, the predictor reconstitutes highly accurate transcriptomes for samples derived from a wide range of tissues and conditions. The broad applicability of the predictor indicates that it recapitulates the quantitative relationships between TFs and target genes ubiquitous across tissues. Significant interacting TF-target gene pairs are extracted from the predictor and enable downstream inference of TF regulators for diverse pathways involved in development, immunity, metabolism, and stress response. A detailed analysis of the hematopoiesis process reveals an atlas of key TFs regulating the development of different hematopoietic cell lineages, and a portion of these TFs are conserved between humans and mice. The results demonstrate that our method is capable of delineating the TFs responsible for fate determination. Compared to other existing tools, EXPLICIT-Human shows a better performance in recovering the correct TF regulators.

A comparative study of the chloroplast genomes of five Lepidium species with high medicinal value.

Plantgenomics is a rapidly developing field in medicinal plant research. This study analysed the relevant information of chloroplasts genome sequences of five medicinal plants from the genus Lepidium . We sequenced the complete chloroplast (cp) genomes of Lepidium apetalum Willd. and Lepidium perfoliatum Linnaeus., and assessed their genetic profiles against the reported profiles of Lepidium sativum Linnaeus., Lepidium meyenii Walp., and Lepidium virginicum Linn. We found that L. apetalum and L. perfoliatum possessed 130 distinct genes that included 85 protein-coding, 37 transfer RNA (tRNA), and eight ribosomal RNA (rRNA) genes. Our repeat analyses revealed that L. apetalum harboured 20 direct repeats, 16 palindrome repeats, 30 tandem repeats, and 87 simple sequence repeats, whereas, L. perfoliatum had 15 direct repeats, 20 palindrome repeats, four reverse repeats, 21 tandem repeats, and 98 simple sequence repeats. Using syntenic analysis, we also revealed a high degree of sequence similarity within the coding regions of Lepidium medicinal plant cp genomes, and a high degree of divergence among the intergenic spacers. Pairwise alignment and single-nucleotide polymorphism (SNP) examinations further revealed certain Lepidium -specific gene fragments. Codon usage analysis showed that codon 14 was the most frequently used codon in the Lepidium coding sequences. Further, correlation investigations suggest that L. apetalum and L. perfoliatum originate from similar genetic backgrounds. Analysis of codon usage bias of Lepidium cp genome was strongly influenced by mutation and natural selection. We showed that L. apetalum and L. perfoliatum will likely enhance breeding, species recognition, phylogenetic evolution, and cp genetic engineering of the Lepidium medicinal plants.