Spatial resolved transcriptomics reveals distinct cross-talk between cancer cells and tumor-associated macrophages in intrahepatic cholangiocarcinoma.

BACKGROUND: Multiple studies have shown that tumor-associated macrophages (TAMs) promote cancer initiation and progression. However, the reprogramming of macrophages in the tumor microenvironment (TME) and the cross-talk between TAMs and malignant subclones in intrahepatic cholangiocarcinoma (iCCA) has not been fully characterized, especially in a spatially resolved manner. Deciphering the spatial architecture of variable tissue cellular components in iCCA could contribute to the positional context of gene expression containing information pathological changes and cellular variability. METHODS: Here, we applied spatial transcriptomics (ST) and digital spatial profiler (DSP) technologies with tumor sections from patients with iCCA. RESULTS: The results reveal that spatial inter- and intra-tumor heterogeneities feature iCCA malignancy, and tumor subclones are mainly driven by physical proximity. Tumor cells with TME components shaped the intra-sectional heterogenetic spatial architecture. Macrophages are the most infiltrated TME component in iCCA. The protein trefoil factor 3 (TFF3) secreted by the malignant subclone can induce macrophages to reprogram to a tumor-promoting state, which in turn contributes to an immune-suppressive environment and boosts tumor progression. CONCLUSIONS: In conclusion, our description of the iCCA ecosystem in a spatially resolved manner provides novel insights into the spatial features and the immune suppressive landscapes of TME for iCCA.

Abundance, characteristics and ecological risk assessment of microplastics in ship ballast water in ports around Liaodong Peninsula, China.

The development of the shipping industry has led to a large volume of ballast water discharge annually. This accelerates pollutants' transfer and dispersion, such as microplastics. Currently, empirical data on microplastics in ballast water are rarely available. This study innovatively investigated the abundance, morphological characteristics (particle size, shape, and color), and polymer composition of microplastics in ballast water from ports surrounding the Liaodong Peninsula. The results revealed that the average abundance of microplastics in 13 ships' ballast water was 6071.30 ± 1313.85 items/m3. Notably, the small microplastics (0.06-2.50 mm) were most abundant, accounting for 94.52 % of the total microplastics. Transparent, fiber, and polyethylene glycol terephthalate were the most prevalent color, shape, and polymer composition of microplastics detected in the ballast water. The risk assessment indicated that these microplastics present ecological risks to organisms. These findings suggest that ship ballast water is the potential "hotspot" for marine microplastics transport.

Diels-Alder Reaction Mechanisms of La@C60 and Gd@C60 Studied Using Density Functional Theory.

Encapsulation of transition metals represents a crucial method for modifying the electronic structure and regulating the reactivity of fullerene, thereby expanding its applications. Herein, we present calculations with density functional theory methods to investigate the mechanisms of the Diels-Alder (DA) reactions of cyclopentadiene and La@C60 or Gd@C60 as well as their tricationic derivatives. Our findings indicate that the encapsulation of La and Gd into the C60 cage is thermodynamically favorable. The DA reactions are favored by the presence of La and Gd, with lower barriers, though the regioselectivity, favoring 6-6 bonds in the fullerene, is not affected. The effect of external electric fields has been also considered.

Facile synthesis of N-doped graphene quantum dots as a fluorescent sensor for Cr(vi) and folic acid detection.

The development of stable fluorescent sensors for toxic pollutants and drugs is meaningful to the environment and public health. In this work, nitrogen-doped graphene quantum dots (N-GQDs) were facially synthesized by a one-step hydrothermal method using soluble starch and l-arginine as carbon and nitrogen sources in pure water at 190 °C for 4 h. The as-synthesized N-GQDs were well characterized and displayed blue fluorescence emission at 445 nm with excellent pH stability, salt tolerance, thermostability, photobleaching resistance and reproducibility. Moreover, N-GQDs could serve as an "on-off" sensor for selective detection of Cr(vi) and folic acid with low detection limit (0.80 and 2.1 µM), good linear correlation over wide linear range (0-50 µM and 0-200 µM) as well as short response time (<10 s). The practical applications of N-GQDs for Cr(vi) and folic acid detection in actual samples were further investigated and showed acceptable recoveries (92-105%) with relative standard deviations less than 5%. These results indicated that this N-GQDs-based sensor could be a potential alternative for Cr(vi) and folic acid detection in the fields of environmental monitoring and drug analysis.

Complete genome sequence of Kushneria phosphatilytica YCWA18T reveals the P-solubilizing activity of the genus Kushneria.

Kushneria phosphatilytica YCWA18T (= CGMCC 1.9149T = NCCB 100306T) was isolated from sediment collected in a saltern on the eastern coast of Yellow Sea in China. The genome was sequenced and comprised of one circular chromosome with the size of 3,624,619 bp and DNA G + C content of 59.13%. A total of 3267 protein-coding genes, 64 tRNA genes and 12 rRNA genes were obtained. Genomic annotation indicated that the genome of K. phosphatilytica YCWA18T had 34 genes involved in phosphorus (P) solubilization/metabolism, e.g., gdh, pqq, phoA, phoD and phoX, which products can convert insoluble P-containing compounds to more bio-available dissolved inorganic P. Comparative genomic analysis of Kushneria strains revealed that gdh, pqq, phoA, phoD and phoX were widely distributed in these strains, indicating the genus Kushneria may play an important role in the P cycle. Additionally, a multitude of salt tolerance genes were detected in the genome of K. phosphatilytica YCWA18T. This study and the genome sequence data will be available for further research and will provide insights into potential biotechnological and agricultural applications of Kushneria strains.

Visible-Light-Driven Reduction of CO2 to CO with Highly Active and Selective Earth-Abundant Metal Porphyrin-Conjugated Organic Polymers.

The field of artificial photosynthesis, which focuses on harnessing solar light for the conversion of CO2 to economically valuable chemical products, remains a captivating area of research. In this study, we developed a series of photocatalysts based on Earth abundant elements (Fe, Co, Ni, Cu, and Zn) incorporated into 2D metalloporphyrin-conjugated organic polymers known as MTBPP-BEPA-COPs. These photocatalysts were utilized for the photoreduction of CO2 employing only H2O as the electron donor, without the need for any sacrificial agents or precious-metal cocatalysts. Remarkably, all of the synthesized MTBPP-BEPA-COPs exhibited an exceptional CO2 photoreduction performance only irradiated by visible light. Particularly, upon optimizing the metal ion coordinated with porphyrin units, ZnTBPP-BEPA-COP outperformed the other MTBPP-BEPA-COPs in terms of photocatalytic activity, achieving an impressive CO reduction yield of 152.18 µmol g-1 after just 4 h of irradiation. The electrostatic potential surfaces calculated by density functional theory suggest the potential involvement of metal centers as binding and catalytic sites for the binding of CO2. The calculated adsorption energy of CO2 with ZnTBPP-BEPA-COP exhibited one of the two smallest values. This may be the reason for the excellent catalytic effect of ZnTBPP-BEPA-COP. Thus, the present study not only demonstrates the potential of porphyrin-based conjugated polymers as highly efficient photocatalysts for CO2 reduction but also offers valuable insights into the rational design of such materials in the future.

Distribution characteristics and ecological risk analysis of microplastics in sediments and effluents related to offshore oil and gas activities in the Bohai Sea, China.

Oil and gas activities are sources of marine microplastics (MPs) but have received less attention globally. This study assessed the distribution characteristics and ecological risks of MPs in 31 sediment samples and effluent samples of 5 oil and gas platforms related to offshore oil and gas activities in the Bohai Sea. The results showed that the mean abundance of MPs in sediment, produced water, and domestic sewage was 205.7 ± 151.5 items/kg d.w., 18 ± 11 items/L, and 26 ± 39 items/L, respectively. The MPs in sediments and effluents were dominated by transparent, rayon, and fibers <1 mm. Oil and gas activities may influence the abundance of MPs in the sediments. The sediments in the area were at a low level of risk, but some samples exhibited indexes beyond low levels. The mass of MPs carried by the effluents from oil and gas platforms in the Bohai Sea was less than that of other sources.

Analysis of Phenotypes Associated with Deficiency of PAX6 Haplotypes in Chinese Aniridia Families.

OBJECTIVE: To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency. METHODS: A comprehensive questionnaire and ophthalmological assessments were administered to both affected patients and unaffected relatives. The clinical feature analysis included the evaluation of visual acuity, intraocular pressure, slit-lamp anterior segment examination, fundus photography, and spectral domain optical coherence tomography. To identify the mutation responsible for aniridia, targeted next-generation sequencing was used as a beneficial technique. RESULTS: A total of 4 mutations were identified, consisting of two novel frameshift mutations (c.314delA, p.K105Sfs*33 and c.838_845dup AACACACC, p.S283Tfs*85), along with two recurring nonsense mutations (c.307C>T, p.R103X and c.619A>T, p.K207*). Complete iris absence, macular foveal hypoplasia, and nystagmus were consistent in these PAX6 haplotype-deficient Chinese aniridia families, while corneal lesions, cataracts, and glaucoma exhibited heterogeneity both among the families and within the same family. CONCLUSION: In our study, two novel PAX6 mutations associated with aniridia were identified in Chinese families, which expanded the phenotypic and genotypic spectrum of PAX6 mutations. We also analyzed the clinical characteristics of PAX6 haplotype deficiency in Chinese aniridia families.

Research Progress on Active Ingredients and Product Development of Lycium ruthenicum Murray.

Lycium ruthenicum Murray possesses significant applications in both food and medicine, including antioxidative, anti-tumor, anti-fatigue, anti-inflammatory, and various other effects. Consequently, there has been a surge in research endeavors dedicated to exploring its potential benefits, necessitating the organization and synthesis of these findings. This article systematically reviews the extraction and content determination methods of active substances such as polysaccharides, anthocyanins, flavonoids, and polyphenols in LRM in the past five years, as well as some active ingredient composition determination methods, biological activities, and product development. This review is divided into three main parts: extraction and determination methods, their bioactivity, and product development. Building upon prior research, we also delve into the economic and medicinal value of Lycium ruthenicum Murray, thereby contributing significantly to its further exploration and development. It is anticipated that this comprehensive review will serve as a valuable resource for advancing research on Lycium ruthenicum Murray.

Detection of Novel BEST1 Variations in Autosomal Recessive Bestrophinopathy Using Third-generation Sequencing.

OBJECTIVE: Autosomal recessive bestrophinopathy (ARB), a retinal degenerative disease, is characterized by central visual loss, yellowish multifocal diffuse subretinal deposits, and a dramatic decrease in the light peak on electrooculogram. The potential pathogenic mechanism involves mutations in the BEST1 gene, which encodes Ca2+-activated Cl- channels in the retinal pigment epithelium (RPE), resulting in degeneration of RPE and photoreceptor. In this study, the complete clinical characteristics of two Chinese ARB families were summarized. METHODS: Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing was performed on the probands to screen for disease-causing gene mutations, and Sanger sequencing was applied to validate variants in the patients and their family members. RESULTS: Two novel mutations, c.202T>C (chr11:61722628, p.Y68H) and c.867+97G>A, in the BEST1 gene were identified in the two Chinese ARB families. The novel missense mutation BEST1 c.202T>C (p.Y68H) resulted in the substitution of tyrosine with histidine in the N-terminal region of transmembrane domain 2 of bestrophin-1. Another novel variant, BEST1 c.867+97G>A (chr11:61725867), located in intron 7, might be considered a regulatory variant that changes allele-specific binding affinity based on motifs of important transcriptional regulators. CONCLUSION: Our findings represent the first use of third-generation sequencing (TGS) to identify novel BEST1 mutations in patients with ARB, indicating that TGS can be a more accurate and efficient tool for identifying mutations in specific genes. The novel variants identified further broaden the mutation spectrum of BEST1 in the Chinese population.

Non-coding RNAs in diabetic peripheral neuropathy: their role and mechanisms underlying their effects.

Diabetic peripheral neuropathy (DPN) is a complication of diabetes with a high rate of disability. However, current clinical treatments for DPN are suboptimal. Non-coding RNAs (ncRNAs) are a type of RNAs that are not translated into proteins. NcRNAs perform functions that regulate epigenetic modifications, transcriptional or post-transcriptional regulators of proteins, and thus participate in the physiological and pathological processes of the body. NcRNAs play a role in the progress of DPN by affecting the processes of inflammation, oxidative stress, cellular autophagy or apoptosis. Therefore, ncRNAs treatment is regarded as a promising therapeutic approach for DPN. In addition, since some ncRNAs present stably in the blood of DPN patients, they are considered as potential biomarkers that contribute to early clinical diagnosis. In this paper, we review the studies on the role of ncRNAs in DPN in the last decade, and discuss the mechanisms of ncRNAs, aiming to provide a reference for the future research on the treatment and early diagnosis of DPN.

Evaluation of nocturnal apnea and airflow limitation as indicators for cognitive dysfunction in patients with chronic obstructive pulmonary disease/obstructive sleep apnea hypopnea syndrome overlap syndrome.

OBJECTIVE: The aim of this study is to investigate how much intermittent hypoxemia and airflow limitation contribute to cognitive impairment in overlap syndrome (OS), which is the coexistence of two common diseases, obstructive sleep apnea hypopnea syndrome (OSAHS) and chronic obstructive pulmonary disease (COPD). METHODS: We conducted a cross-sectional study of patients with OSAHS, COPD or OS, compared with normal controls, to determine the association between sleep apnea/pulmonary function-related indicators and cognitive dysfunction in individuals with OSAHS, COPD or OS. RESULTS: A total of 157 participants were recruited. Both OSAHS and OS presented lower adjusted Montreal cognitive assessment (MoCA) scores compared with COPD group. In addition, the MoCA score was significantly lower in COPD group compared with control group. The incidence of cognitive impairment was 57.4% in OSAHS group, and 78% in OS group, which were significantly higher than COPD group (29%) and control group (8.8%). Furthermore, a broader range of cognitive domains were affected in OS group compared with OSAHS group. Elevated levels of oxygen desaturation index (ODI) and/or apnea hypopnea index (AHI) were positively correlated with increased Epworth sleeping scale (ESS) in OSAHS and OS. Forced vital capacity (FVC), forced expiratory volume in 1 s (FEV1) and peak expiratory flow (PEF) were positively correlated with cognitive scores in OSAHS but not in OS. Serum level of hypoxia-inducible factor-1α (HIF-1α) was significantly higher in OS. Logistic regression identified ODI as an independent risk factor for cognitive impairment in OS, while severity of snoring and PEF were independent risk factors in OSAHS. DISCUSSION: This study revealed significant cognitive impairment in OS, OSAHS and COPD. Sleep-related indicators are warranted in OS patients for detection, differentiation and grading of cognitive impairment, whereas pulmonary functions are warranted in OSAHS patients for detection and early intervention of cognitive impairment.

Versatile Application of TiO2@PDA Modified Filter Paper for Oily Wastewater Treatment.

Although membrane separation technology has been widely used in the treatment of oily wastewater, the complexity and high cost of the membrane preparation, as well as its poor stability, limit its further development. In this study, via the vacuum-assisted suction filtration method, polydopamine (PDA)-coated TiO2 nanoparticles were tightly attached and embedded on both sides of laboratory filter paper (FP). The resultant FP possessed the typical wettability of high hydrophilicity in the air with the water contact angle (WCA) of 28°, superoleophilicity with the oil contact angle (OCA) close to 0°, underwater superoleophobicity with the underwater OCA greater than 150°, and superhydrophobicity under the water with the underoil WCA over 150° for five kinds of organic solvents (carbon tetrachloride, toluene, n-hexane, n-octane, and iso-octane). The separation efficiency of immiscible oil/water, oil-in-water, and water-in-oil emulsions using the modified FP is higher than 99%. After 17 cycles of emulsion separation, a high separation efficiency of 99% was still maintained for the FP, along with good chemical and mechanical stability. In addition, successful separation and purification were also realized for the oil-in-water emulsion that contained the methylene blue (MB) dye, along with the complete degradation of MB in an aqueous solution under UV irradiation.

Highly sensitive and selective detection of triphosgene with a 2-(2'-hydroxyphenyl)benzimidazole derived fluorescent probe.

In this work, a 2-(2'-hydroxyphenyl)benzimidazole derived fluorescent probe, 2-(2'-hydroxy-4'-aminophenyl)benzimidazole (4-AHBI), was synthesized and its fluorescent behavior toward triphosgene were evaluated. The results showed that 4-AHBI exhibited high sensitivity (limit of detection, 0.08 nM) and excellent selectivity for triphosgene over other acyl chlorides including phosgene in CH2Cl2 solution. Moreover, 4-AHBI loaded test strips were prepared for the practical sensing of triphosgene.

Microbial landscapes of the rhizosphere soils and roots of Luffa cylindrica plant associated with Meloidogyne incognita.

Introduction: The root-knot nematodes (RKN), especially Meloidogyne spp., are globally emerging harmful animals for many agricultural crops. Methods: To explore microbial agents for biological control of these nematodes, the microbial communities of the rhizosphere soils and roots of sponge gourd (Luffa cylindrica) infected and non-infected by M. incognita nematodes, were investigated using culture-dependent and -independent methods. Results: Thirty-two culturable bacterial and eight fungal species, along with 10,561 bacterial and 2,427 fungal operational taxonomic units (OTUs), were identified. Nine culturable bacterial species, 955 bacterial and 701 fungal OTUs were shared in both four groups. More culturable bacterial and fungal isolates were detected from the uninfected soils and roots than from the infected soils and roots (except no fungi detected from the uninfected roots), and among all samples, nine bacterial species (Arthrobacter sp., Bacillus sp., Burkholderia ambifaria, Enterobacteriaceae sp., Fictibacillus barbaricus, Microbacterium sp., Micrococcaceae sp., Rhizobiaceae sp., and Serratia sp.) were shared, with Arthrobacter sp. and Bacillus sp. being dominant. Pseudomonas nitroreducens was exclusively present in the infested soils, while Mammaliicoccus sciuri, Microbacterium azadirachtae, and Priestia sp., together with Mucor irregularis, Penicillium sp., P. commune, and Sordariomycetes sp. were found only in the uninfected soils. Cupriavidus metallidurans, Gordonia sp., Streptomyces viridobrunneus, and Terribacillus sp. were only in the uninfected roots while Aspergillus sp. only in infected roots. After M. incognita infestation, 319 bacterial OTUs (such as Chryseobacterium) and 171 fungal OTUs (such as Spizellomyces) were increased in rhizosphere soils, while 181 bacterial OTUs (such as Pasteuria) and 166 fungal OTUs (such as Exophiala) rose their abundance in plant roots. Meanwhile, much more decreased bacterial or fungal OTUs were identified from rhizosphere soils rather than from plant roots, exhibiting the protective effects of host plant on endophytes. Among the detected bacterial isolates, Streptomyces sp. TR27 was discovered to exhibit nematocidal activity, and B. amyloliquefaciens, Bacillus sp. P35, and M. azadirachtae to show repellent potentials for the second stage M. incognita juveniles, which can be used to develop RKN bio-control agents. Discussion: These findings provided insights into the interactions among root-knot nematodes, host plants, and microorganisms, which will inspire explorations of novel nematicides.

Seasonal distribution of microplastics in the surface waters of the Yellow Sea, China.

Different studies are filling the gaps in the distribution map of global marine microplastics. However, the data on the seasonal variation is relatively limited, which may lead to overestimation or underestimation of the distribution level of microplastics. To understand baseline data and seasonal variations of the microplastics in the surface seawater of the Yellow Sea, a survey over four seasons was conducted during 2017-2018. Microplastics were collected using a 330 µm manta net. It was found that the abundance of microplastics was 0.63 ± 0.57 particles/m3. The seasonal abundance variation was spring > summer ≈ winter > autumn. The main categories were foam, line, and fragments, accounting for 32 %, 19 %, and 19 % of the total amount, respectively, and the dominant components were polypropylene, polyethylene, and polyethylene terephthalate, accounting for 38 %, 22 %, and 22 % of particles, respectively. The factors affecting the variation included wind-induced mixing, river input, and environmental topography.

Influence of the casing layer on the specific volatile compounds and microorganisms by Agaricus bisporus.

One of the major variables affecting yield of the mushroom Agaricus bisporus is the casing layer, which directly affects the productivity and mass. Here, volatile organic compounds were extracted by headspace solid-phase microextraction and high-throughput sequencing was used to analyze the microbial community diversity. The relationship between mushroom yield at different cropping stages and the contents of volatile organic compounds and microorganisms in three different casing layers: peat, peat + soil and soil were systematically evaluated. The result shows that Benzaldehyde and (E)-2-octenal which stimulate yield, obviously increased as mushrooms grew, while 3-octanone, which inhibits yield, decreased over time in all three casing layers. However, there was not a strong correlation between the concentration of volatile compounds and yield. In addition, more than 3,000 bacterial operational taxonomic units (OTUs) by performing high throughput sequencing of the microbes were obtained in the three casing layers. Interestingly, the microbial community compositions were very similar between the three casing layers at a later cropping stage, but the community richness varied significantly in different casing layers and at different cropping stages. At the phylum level, the communities had similar structures but were quantitively very different, and this was even more obvious at the genus level. Principal component analysis revealed significant alterations in microbial community structure in different casing layers. Sphingomonas, Dongia and Achromobacter were the dominant genera at cropping stage 1, and the stage 3 were abundant in Saccharibacteria_norank, Pseudomonas, Flavobacterium and Brevundimonas, which was positively correlated with yield, while the abundance of Pseudomonas at stage 1 and Lactococcus and Bacillus at stage 3 was negatively correlated with yield. These results provide a guide for the development and agricultural application of microbial agents for yield improvement in the production of A. bisporus.

[Rapid identification and differential markers of Curcumae Radix decoction pieces of different sources based on Heracles Neo ultra-fast gas phase electronic nose].

Since Curcumae Radix decoction pieces have multiple sources, it is difficult to distinguish depending on traditional cha-racters, and the mixed use of multi-source Curcumae Radix will affect its clinical efficacy. Heracles Neo ultra-fast gas phase electronic nose was used in this study to quickly identify and analyze the odor components of 40 batches of Curcumae Radix samples from Sichuan, Zhejiang, and Guangxi. Based on the odor fingerprints established for Curcumae Radix decoction pieces of multiple sources, the odor components was identified and analyzed, and the chromatographic peaks were processed and analyzed to establish a rapid identification method. Principal component analysis(PCA), discriminant factor analysis(DFA), and soft independent modeling cluster analysis(SIMCA) were constructed for verification. At the same time, one-way analysis of variance(ANOVA) combined with variable importance in projection(VIP) was employed to screen out the odor components with P<0.05 and VIP>1, and 13 odor components such as ß-caryophyllene and limonene were hypothesized as the odor differential markers of Curcumae Radix decoction pieces of diffe-rent sources. The results showed that Heracles Neo ultra-fast gas phase electronic nose can well analyze the odor characteristics and rapidly and accurately discriminate Curcumae Radix decoction pieces of different sources. It can be applied to the quality control(e.g., online detection) in the production of Curcumae Radix decoction pieces. This study provides a new method and idea for the rapid identification and quality control of Curcumae Radix decoction pieces.

Various phenotypes of autosomal dominant cone-rod dystrophy with cone-rod homeobox mutation in two Chinese families.

AIM: To present the clinical manifestations of 5 autosomal dominant cone-rod dystrophy (adCORD) patients from two Chinese families with cone-rod homeobox (CRX) mutation (p.R41W), and to explore the clinical heterogeneity of adCORD with CRX mutation (p.R41W). METHODS: Interrogation and ophthalmological examinations were undertaken in all patients and unaffected members. Analysis of clinical features was performed by visual acuity, slit lamp examination, visual field examination, fundoscopy, autofluorescence and spectral domain optical coherence tomography. Targeted next-generation sequencing was applied as a useful tool to identify the causative mutation of CORD genes. RESULTS: A CRX missense mutation c.121C>T was identified in all patients, resulting in an amino acid change from arginine acid to tryptophan (p.R41W). The patients presented with early onset, progressive and different severities with CORD. CONCLUSION: This is the first report of the clinical phenotype of CRX mutation (p.R41W) in Chinese families, and the mutation can lead to a wide range of various retinal phenotypes.

Visible-Light-Promoted Phosphorylation/Cyclization of 1-Acryloyl-2-cyanoindoles in Green Solvent.

A visible-light-induced persulfate-promoted cascade phosphorylation/cyclization reaction to access various phosphorylated pyrrolo[1,2-a]indolediones under mild conditions was developed. Notably, the transformation was carried out with diethyl carbonate/H2O as a green medium at room temperature. More impressively, traditional metal catalysts and photocatalysts could be effectively avoided. The reactions are simple to operate, easy to scale up, and have good functional group tolerance.