Engineered acetogenic bacteria as microbial cell factory for diversified biochemicals.

Acetogenic bacteria (acetogens) are a class of microorganisms with conserved Wood-Ljungdahl pathway that can utilize CO and CO2/H2 as carbon source for autotrophic growth and convert these substrates to acetate and ethanol. Acetogens have great potential for the sustainable production of biofuels and bulk biochemicals using C1 gases (CO and CO2) from industrial syngas and waste gases, which play an important role in achieving carbon neutrality. In recent years, with the development and improvement of gene editing methods, the metabolic engineering of acetogens is making rapid progress. With introduction of heterogeneous metabolic pathways, acetogens can improve the production capacity of native products or obtain the ability to synthesize non-native products. This paper reviews the recent application of metabolic engineering in acetogens. In addition, the challenges of metabolic engineering in acetogens are indicated, and strategies to address these challenges are also discussed.

Commensal microbiome dysbiosis elicits interleukin-8 signaling to drive fibrotic skin disease.

Wound healing is an intensely studied topic involved in many relevant pathophysiological processes, including fibrosis. Despite the large interest in fibrosis, the network that is related to commensal microbiota and skin fibrosis remains mysterious. Here, we pay attention to keloid, a classical yet intractable skin fibrotic disease to establish the association between commensal microbiota to scaring tissue. Our histological data reveal the presence of microbiota in the keloids. 16S rRNA sequencing characterizes microbial composition and divergence between the pathological and normal skin tissues. Moreover, the data show elevation of interleukin-8 (IL-8) in both the circulation and keloid tissue, which elicited the collagen accumulation and migratory program of dermal fibroblasts via CXCR1/2 receptor. Our research provides insights into the pathology of human fibrotic diseases, advocating commensal bacteria and IL-8 signaling as useful targets in future interventions of recurrent keloid disease.

Robust Nuclear Spin Polarization via Ground-State Level Anticrossing of Boron Vacancy Defects in Hexagonal Boron Nitride.

Nuclear spin polarization plays a crucial role in quantum information processing and quantum sensing. In this work, we demonstrate a robust and efficient method for nuclear spin polarization with boron vacancy (V_{B}^{-}) defects in hexagonal boron nitride (h-BN) using ground-state level anticrossing (GSLAC). We show that GSLAC-assisted nuclear polarization can be achieved with significantly lower laser power than excited-state level anticrossing, making the process experimentally more viable. Furthermore, we have demonstrated direct optical readout of nuclear spins for V_{B}^{-} in h-BN. Our findings suggest that GSLAC is a promising technique for the precise control and manipulation of nuclear spins in V_{B}^{-} defects in h-BN.

Magnon-Skyrmion Hybrid Quantum Systems: Tailoring Interactions via Magnons.

Coherent and dissipative interactions between different quantum systems are essential for the construction of hybrid quantum systems and the investigation of novel quantum phenomena. Here, we propose and analyze a magnon-skyrmion hybrid quantum system, consisting of a micromagnet and nearby magnetic skyrmions. We predict a strong-coupling mechanism between the magnonic mode of the micromagnet and the quantized helicity degree of freedom of the skyrmion. We show that with this hybrid setup it is possible to induce magnon-mediated nonreciprocal interactions and responses between distant skyrmion qubits or between skyrmion qubits and other quantum systems like superconducting qubits. This work provides a quantum platform for the investigation of diverse quantum effects and quantum information processing with magnetic microstructures.

Alginate oligosaccharide assimilation by gut microorganisms and the potential role in gut inflammation alleviation.

Dietary fiber metabolism by gut microorganisms plays important roles in host physiology and health. Alginate, the major dietary fiber of daily diet seaweeds, is drawing more attention because of multiple biological activities. To advance the understanding of alginate assimilation mechanism in the gut, we show the presence of unsaturated alginate oligosaccharides (uAOS)-specific alginate utilization loci (AUL) in human gut microbiome. As a representative example, a working model of the AUL from the gut microorganism Bacteroides clarus was reconstructed from biochemistry and transcriptome data. The fermentation of resulting monosaccharides through Entner-Doudoroff pathway tunes the metabolism of short-chain fatty acids and amino acids. Furthermore, we show that uAOS feeding protects the mice against dextran sulfate sodium-induced acute colitis probably by remodeling gut microbiota and metabolome. IMPORTANCE: Alginate has been included in traditional Chinese medicine and daily diet for centuries. Recently discovered biological activities suggested that alginate-derived alginate oligosaccharides (AOS) might be an active ingredient in traditional Chinese medicine, but how these AOS are metabolized in the gut and how it affects health need more information. The study on the working mechanism of alginate utilization loci (AUL) by the gut microorganism uncovers the role of unsaturated alginate oligosaccharides (uAOS) assimilation in tuning short-chain fatty acids and amino acids metabolism and demonstrates that uAOS metabolism by gut microorganisms results in a variation of cell metabolites, which potentially contributes to the physiology and health of gut.

Tailoring nondiffracting fields with a non-Markovian phase imprint.

We experimentally generate nondiffracting speckles that carry non-Markovian properties by encoding the wavefront of a monochromatic laser beam with ring-shaped non-Markovian phases. The resulting non-Markovian nondiffracting fields present a ring-shaped pattern and central dark notches, which are analyzed with an expression of the orbital angular momentum spectra of the wavefront possessing ring-shaped non-Markovian phases. Furthermore, we demonstrate that the intensity profiles of these non-Markovian nondiffracting fields exhibit stability over multiple Rayleigh ranges, and their statistical properties could be controlled with the non-Markovianity of the input phase masks. This work presents an approach for simultaneously tailoring the diffracting property and non-Markovianity of optical fields and provides a deeper understanding of non-Markovian processes.

Recent progress in engineering Clostridium autoethanogenum to synthesize the biochemicals and biocommodities.

Excessive mining and utilization fossil fuels has led to drastic environmental consequences, which will contribute to global warming and cause further climate change with severe consequences for the human population. The magnitude of these challenges requires several approaches to develop sustainable alternatives for chemicals and fuels production. In this context, biological processes, mainly microbial fermentation, have gained particular interest. For example, autotrophic gas-fermenting acetogenic bacteria are capable of converting CO, CO2 and H2 into biomass and multiple metabolites through Wood-Ljungdahl pathway, which can be exploited for large-scale fermentation processes to sustainably produce bulk biochemicals and biofuels (e.g. acetate and ethanol) from syngas. Clostridium autoethanogenum is one representative of these chemoautotrophic bacteria and considered as the model for the gas fermentation. Recently, the development of synthetic biology toolbox for this strain has enabled us to study and genetically improve their metabolic capability in gas fermentation. In this review, we will summarize the recent progress involved in the understanding of physiological mechanism and strain engineering for C. autoethanogenum, and provide our perspectives on the future development about the basic biology and engineering biology of this strain.

Screening of astaxanthin-overproducing Xanthophyllomyces dendrorhous strains via iterative ARTP mutagenesis and cell sorting by flow cytometry.

AIMS: The astaxanthin-producing yeast Xanthophyllomyces dendrorhous is widely used in aquaculture. Due to the production of carotenoid, this yeast shows visible color; however, high-throughput approaches for identification of astaxanthin-overproducing strains remain rare. METHODS AND RESULTS: This study verified an effective approach to identify astaxanthin-overproducing mutants of X. dendrorhous by flow cytometry (FCM) and cell sorting. First, the mutant libraries were generated by atmospheric and room-temperature plasma (ARTP) mutagenesis. Second, a highly direct correlation between the concentrations of intracellular astaxanthin and the levels of emitting fluorescence was constructed by testing a variety of astaxanthin-contained populations via FCM and cell sorting. Third, iterative cell sorting efficiently improves the identification of astaxanthin-overproducing strains. Finally, two mutants producing 4.96 mg astaxanthin g-1 DCW (dry cell weight) and 5.30 mg astaxanthin g-1 DCW were obtained, which were 25.3% and 33.8% higher than that of the original strain, respectively. CONCLUSIONS: This study demonstrated that iterative ARTP mutagenesis along with cell sorting by FCM is effective for identifying astaxanthin-overproduction strains.

Single-pixel transmission matrix recovery via two-photon fluorescence.

Imaging at depth in opaque materials has long been a challenge. Recently, wavefront shaping has enabled notable advance for deep imaging. Nevertheless, most noninvasive wavefront-shaping methods require cameras, lack the sensitivity for deep imaging under weak optical signals, or can only focus on a single "guidestar." Here, we retrieve the transmission matrix (TM) noninvasively using two-photon fluorescence exploiting a single-pixel detection combined with a computational framework, allowing to achieve single-target focus on multiple guidestars spread beyond the memory effect range. In addition, if we assume that memory effect correlations exist in the TM, we are able to substantially reduce the number of measurements needed.

A pancancer analysis of the clinical and genomic characteristics of multiple primary cancers.

Multiple primary cancer (MPC) denotes individuals with two or more malignant tumors occurring simultaneously or successively. Herein, a total of 11,000 pancancer patients in TCGA database (1993-2013) were divided into MPC or non-MPC groups based on their history of other malignant tumors. The incidence of MPC has risen to 8.5-13.1% since 2000. Elderly individuals, males, early-stage cancer patients, and African Americans and Caucasians are identified as independent risk factors (p < 0.0001). Non-MPC patients exhibit significantly longer overall survival (OS) and disease-free survival (DFS) (p = 0.0038 and p = 0.0014). Age (p < 0.001) and tumor staging at initial diagnosis (p < 0.001) contribute to this difference. In our center, MPC was identified in 380 out of 801 tumor events based on SEER criteria. The peak occurrence of secondary primary was about 1-5 years after the first primary tumor, with a second small peak around 10-15 years. Multiple tumors commonly occur in the same organ (e.g., breast and lung), constituting 12.6%. Certain cancer types, notably skin cutaneous melanoma (SKCM), exhibit significantly higher tumor mutational burden (TMB) in the MPC group (17.31 vs. 6.55 mutations/MB, p < 0.001), with high TMB associated with improved survival (p < 0.001). High TMB in MPC may serve as a predictor for potential immunotherapy application.

The horizontal gene transfer of perchlorate reduction genomic island in three bacteria from an ecological niche.

Three new strains of dissimilatory perchlorate-reducing bacteria (DPRB), QD19-16, QD1-5, and P3-1, were isolated from an active sludge. Phylogenetic trees based on 16S rRNA genes indicated that QD19-16, QD1-5, and P3-1 belonged to Brucella, Acidovorax, and Citrobacter, respectively, expanding the distribution of DPRB in the Proteobacteria. The three strains were gram-negative and facultative anaerobes with rod-shaped cells without flagella, which were 1.0-1.6 µm long and 0.5-0.6 µm wide. The three DPRB strains utilized similar broad spectrum of electron donors and acceptors and demonstrated a similar capability to reduce perchlorate within 6 days. The enzyme activity of perchlorate reductase in QD19-16 toward chlorate was higher than that toward perchlorate. The high sequence similarity of the perchlorate reductase operon and chlorite dismutase genes in the perchlorate reduction genomic islands (PRI) of the three strains implied that they were monophyletic origin from a common ancestral PRI. Two transposase genes (tnp1 and tnp2) were found in the PRIs of strain QD19-16 and QD1-5, but were absent in the strain P3-1 PRI. The presence of fragments of IR sequences in the P3-1 PRI suggested that P3-1 PRI had previously contained these two tnp genes. Therefore, it is plausible to suggest that a common ancestral PRI transferred across the strains Brucella sp. QD19-16, Acidovorax sp. QD1-5, and Citrobacter sp. P3-1 through horizontal gene transfer, facilitated by transposases. These results provided a direct evidence of horizontal gene transfer of PRI that could jump across phylogenetically unrelated bacteria through transposase. KEY POINTS: • Three new DPRB strains can effectively remove high concentration of perchlorate. • The PRIs of three DPRB strains are acquired from a single ancestral PRI. • PRIs are incorporated into different bacteria genome through HGT by transposase.

Identification of a Novel Hepacivirus in Southeast Asian Shrew (Crocidura fuliginosa) from Yunnan Province, China.

The genus Hepacivirus contains single-stranded positive-sense RNA viruses belonging to the family Flaviviridae, which comprises 14 species. These 14 hepaciviruses have been found in different mammals, such as primates, dogs, bats, and rodents. To date, Hepacivirus has not been reported in the shrew genus of Crocidura. To study the prevalence and genetic evolution of Hepacivirus in small mammals in Yunnan Province, China, molecular detection of Hepacivirus in small mammals from Yunnan Province during 2016 and 2017 was performed using reverse-transcription polymerase chain reaction (RT-PCR). Our results showed that the overall infection rate of Hepacivirus in small mammals was 0.12% (2/1602), and the host animal was the Southeast Asian shrew (Crocidura fuliginosa) (12.5%, 2/16). Quantitative real-time PCR showed that Hepacivirus had the highest viral RNA copy number in the liver. Phylogenetic analysis revealed that the hepaciviruses obtained in this study does not belong to any designated species of hepaciviruses and forms an independent clade. To conclude, a novel hepacivirus was identified for the first time in C. fuliginosa specimens from Yunnan Province, China. This study expands the host range and viral diversity of hepaciviruses.

High-level production of nervonic acid in the oleaginous yeast Yarrowia lipolytica by systematic metabolic engineering.

Nervonic acid benefits the treatment of neurological diseases and the health of brain. In this study, we employed the oleaginous yeast Yarrowia lipolytica to overproduce nervonic acid oil by systematic metabolic engineering. First, the production of nervonic acid was dramatically improved by iterative expression of the genes ecoding ß-ketoacyl-CoA synthase CgKCS, fatty acid elongase gELOVL6 and desaturase MaOLE2. Second, the biosynthesis of both nervonic acid and lipids were further enhanced by expression of glycerol-3-phosphate acyltransferases and diacylglycerol acyltransferases from Malania oleifera in endoplasmic reticulum (ER). Third, overexpression of a newly identified ER structure regulator gene YlINO2 led to a 39.3% increase in lipid production. Fourth, disruption of the AMP-activated S/T protein kinase gene SNF1 increased the ratio of nervonic acid to lignoceric acid by 61.6%. Next, pilot-scale fermentation using the strain YLNA9 exhibited a lipid titer of 96.7 g/L and a nervonic acid titer of 17.3 g/L (17.9% of total fatty acids), the highest reported titer to date. Finally, a proof-of-concept purification and separation of nervonic acid were performed and the purity of it reached 98.7%. This study suggested that oleaginous yeasts are attractive hosts for the cost-efficient production of nervonic acid and possibly other very long-chain fatty acids (VLCFAs).

A preliminary evaluation of targeted nanopore sequencing technology for the detection of Mycobacterium tuberculosis in bronchoalveolar lavage fluid specimens.

Objective: To evaluate the efficacy of targeted nanopore sequencing technology for the detection of Mycobacterium tuberculosis(M.tb.) in bronchoalveolar lavage fluid(BALF) specimens. Methods: A prospective study was used to select 58 patients with suspected pulmonary tuberculosis(PTB) at Henan Chest Hospital from January to October 2022 for bronchoscopy, and BALF specimens were subjected to acid-fast bacilli(AFB) smear, Mycobacterium tuberculosis MGIT960 liquid culture, Gene Xpert MTB/RIF (Xpert MTB/RIF) and targeted nanopore sequencing (TNS) for the detection of M.tb., comparing the differences in the positive rates of the four methods for the detection of patients with different classifications. Results: Among 58 patients with suspected pulmonary tuberculosis, there were 48 patients with a final diagnosis of pulmonary tuberculosis. Using the clinical composite diagnosis as the reference gold standard, the sensitivity of AFB smear were 27.1% (95% CI: 15.3-41.8); for M.tb culture were 39.6% (95% CI: 25.8-54.7); for Xpert MTB/RIF were 56.2% (95% CI: 41.2-70.5); for TNS were 89.6% (95% CI: 77.3-96.5). Using BALF specimens Xpert MTB/RIF and/or M.tb. culture as the reference standard, TNS showed 100% (30/30) sensitivity. The sensitivity of NGS for pulmonary tuberculosis diagnosis was significantly higher than Xpert MTB/RIF, M.tb. culture, and AFB smear. Besides, P values of <0.05 were considered statistically significant. Conclusion: Using a clinical composite reference standard as a reference gold standard, TNS has the highest sensitivity and consistency with clinical diagnosis, and can rapidly and efficiently detect PTB in BALF specimens, which can aid to improve the early diagnosis of suspected tuberculosis patients.

Analysis of Nucleoporin 107 Overexpression and Its Association with Prognosis and Immune Infiltration in Lung Adenocarcinoma by Bioinformatics Methods.

Background: Lung adenocarcinoma (LUAD) has high morbidity and mortality. Current studies indicate nucleoporin 107 (NUP107) is involved in the construction of nuclear pore complex, and NUP107 overexpression contributes to the growth and development in most types of cancers, but its effect in LUAD has not been elucidated. Methods: Differences in NUP107 expression were investigated using the Cancer Genome Atlas (TCGA) and multiple Gene Expression Omnibus (GEO) data sets. Enrichment analysis were implemented to probe the NUP107 function. The association of NUP107 with the degree of immune cell infiltration was investigated by the TIMER database, single-sample gene set enrichment analysis (ssGSEA), and ESTIMATE. The association of NUP107 expression with tumor mutation burden (TMB), TP53, and immune checkpoint was analyzed. Single-cell RNA sequencing data were used to detect NUP107 expression in different cell clusters. Finally, we performed real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry (IHC) to prove the difference of NUP107 expression. Results: NUP107 was overexpressed in LUAD and mainly expressed in cancer stem cell (CSC). Overexpression of NUP107 in LUAD suggested a poorer prognosis. Functional enrichment analysis pointed out that NUP107 was mainly linked to the regulation of cell cycle. Both immune cell infiltration and TMB were found to be in connection with NUP107. Cases in the group with high NUP107 expression had poorer immune infiltration, but had higher expression of immune checkpoints, TMB, and proportion of TP53 mutations. Conclusion: NUP107 is a sensitive diagnostic and prognostic factor for LUAD and may be involved in tumor progression through its effects on cell cycle and immune infiltration.

Advances in synthetic biology toolboxes paving the way for mechanistic understanding and strain engineering of gut commensal Bacteroides spp. and Clostridium spp.

The gut microbiota plays a significant role in influencing human immunity, metabolism, development, and behavior by producing a wide range of metabolites. While there is accumulating data on several microbiota-derived small molecules that contribute to host health and disease, our knowledge regarding the molecular mechanisms underlying metabolite-mediated microbe-host interactions remains limited. This is primarily due to the lack of efficient genetic tools for most commensal bacteria, especially those belonging to the dominant phyla Bacteroides spp. and Clostridium spp., which hinders the application of synthetic biology to these gut commensal bacteria. In this review, we provide an overview of recent advances in synthetic biology tools developed for the two dominant genera, as well as their applications in deciphering the mechanisms of microbe-host interactions mediated by microbiota-derived small molecules. We also discuss the potential biomedical applications of engineering commensal bacteria using these toolboxes. Finally, we share our perspective on the future development of synthetic biology tools for a better understanding of small molecule-mediated microbe-host interactions and their engineering for biomedical purposes.

Trends and hotspots in critical thinking research over the past two decades: Insights from a bibliometric analysis.

Critical thinking has received significant scholarly attention in education over the years. This study conducted a bibliometric analysis of critical thinking during the last two decades (2000-2021) to identify research trends and hotspots of critical thinking. After data processing, 2043 publications related to critical thinking were retrieved from the Web of Science (WOS). Our analysis covers the number of publications per year, most used keywords, most productive countries/regions, institutions and authors, and most cited publications. The results show that critical thinking received increasing interest throughout this period; the research topics of critical thinking were rich and constantly evolving; the publications in western countries/regions have a stronger impact and higher recognition than do those in non-western countries; and critical thinking instruction has become the most popular research topic. This study holds important implications and should serve as a reference for future research.

[Genetic modification of acetogens and optimization of fermentation process in C1-gas bioconversion].

The current linear economy model relies on fossil energy and increases CO2 emissions, which contributes to global warming and environmental pollution. Therefore, there is an urgent need to develop and deploy technologies for carbon capture and utilization to establish a circular economy. The use of acetogens for C1-gas (CO and CO2) conversion is a promising technology due to high metabolic flexibility, product selectivity, and diversity of the products including chemicals and fuels. This review focuses on the physiological and metabolic mechanisms, genetic and metabolic engineering modifications, fermentation process optimization, and carbon atom economy in the process of C1-gas conversion by acetogens, with the aim to facilitate the industrial scale-up and carbon negative production through acetogen gas fermentation.

Overexpression of plastid lipid-associated protein in marine diatom enhances the xanthophyll synthesis and storage.

Plastoglobules, which are lipoprotein structures surrounded by a single hydrophobic phospholipid membrane, are subcellular organelles in plant chromoplasts and chloroplasts. They contain neutral lipids, tocopherols, quinones, chlorophyll metabolites, carotenoids and their derivatives. Proteomic studies indicated that plastoglobules are involved in carotenoid metabolism and storage. In this study, one of the plastid lipid-associated proteins (PAP), the major protein in plastoglobules, was selected and overexpressed in Phaeodactylum tricornutum. The diameter of the plastoglobules in mutants was decreased by a mean of 19.2% versus the wild-type, while the fucoxanthin level was increased by a mean of 51.2%. All mutants exhibited morphological differences from the wild-type, including a prominent increase in the transverse diameter. Moreover, the unsaturated fatty acid levels were increased in different mutants, including an 18.9-59.3% increase in eicosapentaenoic acid content. Transcriptomic analysis revealed that PAP expression and the morphological changes altered xanthophyll synthesis and storage, which affected the assembly of the fucoxanthin chlorophyll a/c-binding protein and expression of antenna proteins as well as reduced the non-photochemical quenching activity of diatom cells. Therefore, metabolic regulation at the suborganelle level can be achieved by modulating PAP expression. These findings provide a subcellular structural site and target for synthetic biology to modify pigment and lipid metabolism in microalgae chassis cells.

Spin Defects in hBN assisted by Metallic Nanotrenches for Quantum Sensing.

The omnipresence of hexagonal boron nitride (hBN) in devices embedding two-dimensional materials has prompted it as the most sought after platform to implement quantum sensing due to its testing while operating capability. The negatively charged boron vacancy (VB-) in hBN plays a prominent role, as it can be easily generated while its spin population can be initialized and read out by optical means at room-temperature. But the lower quantum yield hinders its widespread use as an integrated quantum sensor. Here, we demonstrate an emission enhancement amounting to 400 by nanotrench arrays compatible with coplanar waveguide (CPW) electrodes employed for spin-state detection. By monitoring the reflectance spectrum of the resonators as additional layers of hBN are transferred, we have optimized the overall hBN/nanotrench optical response, maximizing thereby the luminescence enhancement. Based on these finely tuned heterostructures, we achieved an enhanced DC magnetic field sensitivity as high as 6 × 10-5 T/Hz1/2.